What you say is true, but they DON'T play them every week.
Where the teams you mention in the bigger conferences play 2-4 patsies a year, Boise State and TCU play 2-3 decent teams a year and the rest of their schedule is filled with patsies.
This is not meant to disrespect Boise State or TCU, I think they deserve a chance to play in a PLAYOFF system. That would eliminate the issue.
You don't think there are weak sisters in the Big 10 or SEC? For years Northwestern couldn't win a game. Indiana is always on the bottom and with the exception of a year or 2, so is Minnesota. And Boise St. can't help their conference but the truth to the matter is, they are a powerhouse team over the last few years. As was said, the established conferences want the whole pie for themselves and hate it that teams like Boise and TCU have been this competitive. These are the same arguments that used to be made in the 80's when BYU and Clemson won national titles.