Todd, I think you are digging a little deeper than is required on this one. I believe the easiest common denominator for "respect" from the media is winning on the road, which everyone acknowledges is very difficult in the NFL. You brought up our dominance during the past decade, however (I am going off memory here after looking this up over three years ago) we only won 4 games on the road against teams that finished the season at or above .500 during the 2003-07 seasons combined. The Niners get as much respect as they do right now, because last season they won three games on the road against teams that finished at or above .500.
Of course I have argued the ratings angle dozens of times on this site as well. It isn't tied into market size but merchandise sales which we are constantly in the bottom half of the league in. If your programming isn't catering to the actual consumers of NFL products then you won't last long as a network.