I doubt it is just that.
Think about how we classify 49er fans. Mainly because of some absolute idiots in their fanbase. It rightfully annoy the hell out of the reasonable fans because nobody likes being thrown in the box with a bunch of idiots.
Then again, we have some fans that act like we have already won 5 super bowls and are also slated to win the World Series and NBA championship. I can imagine that would get annoying, since it annoys me and I am a Seahawk fan. Yeah, if I was an opposing fan I would start to have a very low opinion of Seahawks fans - not because of the majority of the fanbase but because a very vocal, very confused, and very loud minority has gone beyond giddy to completely out of their freaking mind annoying.
But again, while our idiots in the minority say ridiculous things on message boards and accost people in the stands for wearing the wrong color jerseys, their idiots stab people. They win hands down in the idiot department for that.
Frankly, last year in the second half of the year we were not just good, we were record book breaking dominant. If we had not given up that last drive to Atlanta - Wilson would be even more venerated than he is (for that amazing comeback) and we probably would have rode into Candlestick on that wave of momentum and stomped them. That was one of the best teams I have seen in a while.
But we didn't, so the 49ers went to the SB and after losing are rewarded by hearing everyone pay more attention to the Seahawks instead of them. Nevermind that the 49ers have the best LB corps in the game, one of the best starting defensive lines in the game and one of the better coaches in the game - combined with a QB that only started half a year and led his team to the SB (which makes him undefeated in playoff games). They can rightfully expect to be better for the same reason we expect Wilson to be better - QBs don't peak their first few years.
The 49ers fans feel slighted by the lack of attention and respect, and they feel some of our fans are insufferable. And they are right.
We feel they have more idiots and worse idiots than most other fanbases, and that they are pretty full of themselves for a team that hasn't won a SB since half their fans were in diapers. Yeah they won plenty, back when nobody on the team now was playing and back when half the fans don't even remember. So what?
The funny part is that we probably hate each other most because we are almost mirrors of each other in certain ways and would probably make the other team our 2nd favorite if that team was in an opposing conference - but we are chasing the same ring so they are the enemy.