The story of the Luftwaffe is very interesting. A great deal of them had no interest in war, no interest in serving Hitler, and no feeling that they were connected to the German Army as it was. I've studied this stuff for years and it always amazes me what happened. I am an educator by trade with a subject specialization (like a double minor) in social studies, with a specific emphasis on history. My father was a history teacher, and he homeschooled me for a while in high school after he retired due to a bad few injuries that kept me from going to school. He'd assign me books on World War II for history and we'd discuss them. Books from all points of view. Novels included. We'd have very spirited discussions, in particular due to our family heritage (we are half German).
The German "juggernaut" was so fractured. You had the SS, the Gestapo, the German Army, The Luftwaffe (Air Force), The Kriegsmarine, and others. Known together they were the "Wehrmacht". But there were even deeper levels and other intelligence gathering agencies. What ultimately ended up happening was nobody trusted anybody else, and everybody thought everybody else was a member of one of the groups that was ratting out others for not being true party members, etc. This of course led to everybody feeling forced into joining "the Party" - The Nazis.
The Luftwaffe specifically had a pretty proud tradition and had many men who had fought in World War I and had determined at the end of the war that they had no interest in doing it again. They were glad it was over, they were exhausted, and they were still men of honor for the most part, who had conceded to many things as part of their total surrender at the end of World War I. They were put in a terrible position by the rest of the Wehrmacht, which as you say was controlled by the SS who were the "new guard" and were supposedly righting the wrongs of the surrender at the end of the Great War.
The big issue is that the Luftwaffe, while still members of the Wehrmacht, also felt compelled to follow the "fair rules of war" for the most part. Many of them were as committed to the Geneva Convention Treaties, because those were the terms under which they surrendered.
Many of the POW's that were shot down over Britain were seemingly glad, because the British followed the Geneva Convention and allowed things such as Red Cross relief, health treatment, and general respect for leaders and such. Although the TV show Hogan's Heroes made a pretty big joke out of it all, they actually had quite a bit historically correct. It was a comedy based on "The Great Escape" which was written by an actual POW and did take place. Prisoners of war are treated differently than spies. Spies are those who snuck into countries without uniform. In uniform, you could not technically be tried as a spy and executed. Those were the rules. The Luftwaffe for the most part observed these agreed upon standards within Germany and its "territories" as did the British (and Americans as the US Army Air Force got involved and became integrated with the Royal Air Force or RAF). The Luftwaffe made an effort to look out for other pilots in a sense and get them into Luftwaffe prison camps as soon as possible so that they were protected under the Geneva Conventions.
The big issue, and one that people don't understand (and sorry I'm going on about this) is that the POW camps were run pretty fairly for the most part for the majority of the war. Much of the Luftwaffe were unwilling participants that were "drafted" out of areas that Germany had overtaken such as Austria/Hungary, and so on. If a plane was shot down then the SS/Gestapo would attempt to get to them and then kill them and claim to the Swiss and Red Cross that they were spies who had parachuted in, weren't in uniform and were shot while attempting to escape. Of course this was all a big fat lie as TRICHAWK discusses above. The Luftwaffe didn't want this, because they were going on bombing runs over London daily and didn't want to be exposed to torture and such if they were taken down by flak.
What Germany did, and the sickness of this whole thing is that you can NOT torture political prisoners or prisoners of war. They are bound by the Geneva Conventions, monitored by the Red Cross and in WWII the Swiss to assure that POW's were treated properly. What Germany did was conquer countries in short order like France and Poland and on and on, even attempting to take over North Africa and ever expanding to the west in an attempt to overtake England and to the east in order to overtake Russia. The "rules" say that you can do what you want to your own citizens (at least they did before the 1949 Geneva Conventions). So the Germans literally felt fully justified in putting the Poles in concentration camps (death camps). Due to the rules of war, they had rightfully conquered Poland, making them their own citizens, and they were allowed to treat them as they wished. Think of that. They would conquer a country and then wipe out millions of people because they felt they now had the legal and somehow moral standing to do so because they were their own "people". It's disgusting, but that's what happened. That's why there were two sets of rules in the camps, and a big reason why the Luftwaffe at times did things that may have seen "unPatriotic" to the Nazis (if you can even think of acting against them as being unpatriotic.... but I hope you get the gist), but they felt that as pilots, as soldiers, as human beings, and as an independent air force that had been established with honor and dignity and respect long before the rest of the Wehrmacht, in particular the SS/Gestapo, then they were going to do things differently. Of course there were many members of the Luftwaffe that were dyed in the wool members of the Nazi party and were angry at the results of World War I and Germany "caving" (thus Hitler's rise to power as he rallied the younger people and many ex-soldiers like himself into an absolute frenzy of hate over how Germany had been sold out by their leaders and steamrolled by the allies).
It still amazes me to this day how much took place there, and how quickly and seemingly easily the Nazis controlled things and were able to put in the puppet Vischi regime in France and conquer it in days. To overtake Poland and erect the Warsaw ghettos so quickly, and were able to align themselves with Italy, Japan, and others and proceed on a 10 year or so build-up to war without anybody taking much notice (and creating a massive war machine with tunnels and underground bomb proof housing for hundreds of thousands, and on and on) and were led by a maniac and a series of other maniacs who were all addicted to morphine and were occultists that felt it was their duty to "cleanse the earth" and begin a thousand year reich to run the world in their way.
The craziest bit of it all is that they had conquered the majority of Europe, and if not for Hitler's insanity and thoughts that he could conquer Russia that he very well may have controlled all of Europe with the exception of England and everything to the Russian border, and the entirety of Northern Africa if he had essentially stopped without pissing off the Russians. He had pretty much accomplished that, but with his further insanity and declaration of war on the United States and Japan attacking Pearl Harbor, then the combination of the US/England Army Air Force and RAF... remember, the US Air Force hadn't even been officially formed yet, they were still a division of the Army with not nearly the funding or R&D that was needed, despite the protestations of General Billy Mitchell in the 1920's and 1930's warning of just such a situation happening and the vast importance of putting all effort into the building of a separate Air Force with bombers that were capable of taking out sea going vessels with ease (Congress and other Generals disagreed and scoffed at Mitchell, despite his demonstrations of air superiority on decommissioned battleships) immediately to prepare for a war that he and many others who followed him saw coming. The combo of the AAF/RAF and the Russian Air Force and ultimately the sheer numbers of Russian foot soldiers and tanks who were able to march through Berlin and end the war, and of course the US and British Soldiers who set the tone for that event to come by their actions at Normandy.
I know I've kind of veered off the tracks, but this stuff fascinates me, and I have to exercise my WWII muscle now and again. But I think it is just so interesting how it played out, and to end it all out, the further insanity, where those such as Goering, Himler, and others literally thought (talk about DELUSIONAL) that they could sit down and negotiate a peace treaty with Churchill and FDR and Truman. They literally thought they would meet up somewhere and discuss the idea that the Nazis could maintain any already conquered countries including much of Europe (that they were losing as all that was left of their Army was essentially the Hitler Youth and old men who were in their World War I uniforms and were activated in the last days to "defend Berlin" for Hitler as if he would re-configure and take control again. It was stunning how insane they all were, yet they were able to control the actions and deeds of millions of people and take the lives of millions more. It's a lesson that I hope never goes by the wayside. I hope that those watching what is happening around the world will realize the importance of what our military does and why they do it, whether they agree with it or not. My wife grew up in Germany on a military base and was treated wonderfully. The people by and large were grateful to have many military bases in then West Germany to keep such a thing from ever happening again. But just looking back on it, it is astounding.
I want to just wrap back around to the pilots of the Luftwaffe and say that I've read many stories of their gallantry and noble deeds and at the very least, their recognition of the importance of the rules of war and following the protocol that had been established, and their separation from the ground troops and ability to see that what was happening within Hitler's regime was crazy by many. There were those who resisted and spied against the Nazis from within throughout the entire war and were pivotal in sending information to the allies that helped turn the tide of the war, but let's not ever forget the actions of those who disobeyed orders and did what they knew to be right, or at the very least did their duty as they saw fit, but also respected the fact that soldiers they captured and put in Luftwaffe camps were to be treated with dignity and respect and NOT turned over to the Gestapo by any means. In the story of the Great Escape you see that the Gestapo eventually came and took the Luftwaffe commander (Komandant) and executed him for doing just the things were talking about. He didn't execute POW's who were caught trying to escape, for he knew it was their duty as soldiers to attempt to escape and assist their forces. This is what led to his death as the SS further devolved into just flat out not even pretending to follow the Geneva Conventions. The Allies treated the Luftwaffe soldiers who were captured this same way. There is a dignity, common respect, and code of conduct that many pilots followed. Don't let it come across as I'm defending Nazis. Because I am certainly not. But there were those just as Aros points out in his original post that understood the difference between right and wrong and saw their duty to fellow humans and specifically pilots to be more important than following orders from an obvious nutjob who had no respect, dignity, or sanity and was just a power hungry psychopath, sociopath, murderer, and on and on. I can't even come up with words to describe the horrific "humans" that Hitler, Himler, Goering, Rommel, and others were. It's just not something I can even fathom. But it sure is interesting stuff.
I'd love any corrections or additions to what I've whipped out here, because this is my recollection from readings I did 20 years ago and discussions I had with my father. He was as Patriotic of an American as there ever was, but... he also gave me the straight scoop on things and backed it up with writings from very involved people. I also discussed it to a limited extent with my Grandpa Buzz who I mentioned earlier, who didn't say a whole lot, but when he did.... people listened. By the way... we're going to dig out old photos of him and his plane and such this weekend I hope and hopefully we can see what he was flying and I can learn a bit more about how he did his job and all that went into it.
Good reading for sure... on a Seahawks football board of all places. The knowledge here never ceases to amaze me!

R.I.P. Dad. I miss you. You will never be forgotten
1/12/39 - 8/7/08