Here's the thing. College football is the only sport I can think of in the world that's set up this way. Whether it's the BCS system or the committee doing the selecting, what it comes down to is that 130 teams play a relatively short schedule of games, and then 126 of them are eliminated, in its current state, by a committee of people who "think" one team is better than another.
Yes, you have selection committees in other sports, but even in March Madness, the conference tournament winners earn their way in by winning the title. Then the committee fills in the balance of 68 teams subjectively.
They can ramble on about the factors they use to determine their selections, but at the end of the day it's really nothing more than the eye test, which most certainly includes personal bias toward certain teams and conferences.