This is a discussion. Also, a big thing of all this has to do with conference strength.
The Pac-10 is generally viewed as being somewhat weaker than the other conferences so USC made up for it by dominating their conference as well as an 11 point victory over Virginia Tech which managed to stick with people when Hokies started taking over the ACC.
Oklahoma went undefeated in the Big XII which was no small feat, but also had a pretty dominating performance over Oregon when the Ducks supposedly had a good look going into the 2004 season, as well as shutting out Texas.
Auburn's three nonconference games were Louisiana Monroe, The Citadel and Louisiana Tech. Not exactly the best teams to play when in the hunt for a national championship. The SEC got a pretty poor gauge of conference strength in 2004 because most of the teams in the SEC played very low-ranked I-A teams or I-AA teams in their nonconference schedules. Georgia was generally viewed as the only national powerhouse team that the SEC would generate after Oregon State beat LSU for all intents and purposes, but the hopes for the Bulldogs disappeared after the Vols beat Georgia Between The Hedges.
Auburn's blowout victory over Tennessee at Neyland didn't help much, either. Tennessee had a flukey-looking win over Florida and an impressive but still narrow-margined victory over Georgia, and after they lost to Auburn, the game said more about Tennessee perhaps not being as good as their record suggested, moreso than Auburn being really good.
Auburn's final two SEC games, against Alabama and Tennessee didn't help their cause much as both games were far closer than they were predicted to be while Oklahoma had an impressive win over Colorado and USC had one of their own over Notre Dame (Notre Dame beat Tennessee who gave Auburn a heck of a scare in the SECCG; that's the direct effect Battle For Shillelagh had on the SEC).
Not detracting anything from Auburn on my part, going undefeated in the SEC is a mighty impressive thing to do. I'm just trying to cast some insight as to why Oklahoma and USC were picked for the national championship over Auburn. I don't pretend to be able to make any predictions before-the-fact of who should have played in Miami. To do such a thing this year would be impossible -- The case for each team was equally as strong. Auburn didn't get snubbed because of bias -- They just failed to shine when USC and Oklahoma did. The BCS sucks, but under this system, that's how it works. You have to win impressively every week.