Imagine if you put the Patiots, Colts, and Chargers into NCAA football. Then imagines they all played eachother and each went 1-1 within the group, but they won all their other games and each finished 10-1.
So then, would you tell me, that Boston College and Ohio State are more legitimate BCS Championship contenders because "a loss is a loss you wussy losing whiner NFL teams" and that Boston College would probably slaughter the Patriots anyway, since San Diego exposed them with that overtime defeat?
A loss is a loss and a win is a win in the sense that a coin is a coin and a check is check. Their value varies. No team can go perfect in the NFL since like 1972 or something. Conferences like the SEC and Pac-10 can be almost as difficult in years where many of their programs are healthy. Other conferences have far fewer competitive programs.
And if you dont think its fair to compare NFL teams because they are so much better than any NCAA team, consider that a 1 loss Florida team beat an undefeated Ohio State 41-14 in the last BCS Championship. If the best team in the SEC played the best team in say the NFC West, they would probably only lose about 41-14. So the difference between the SEC and the Big 10 is very similar to the difference between the lower tiers of the NFL and the SEC.
Also, lets talk about the SEC's 'losing record in bowl games the last 5 years' that someone mentioned and LSU scheduling the might Tulane as an out of conference opponent while OSU scheduled Washington who used to be good. LSU scheduled Virginia Tech. One or two top level programs is enough. Now, LSU scheduled Tulane, who plays in New Orleans, to help Tulane and because fans like it, as they are a popular local program and there is an ancient rivalry. It is not OSU's fault if none of their out of conference opponents are ranked this year, but the nature of the gamble is that if you dont schedule teams that turn out to be good and your conference falls apart, you do not prove much, and you cannot objectively be said to have proved more than a team that played many tough opponents and only lost 1 close game to one of those opponents. Now, the bowl record. Half the teams in the SEC may make a bowl in a given year. Among recent SEC bowl appearances I remember LSU beating Oklahoma in the 2004 BCS, an undefeated Auburn that should have split the national championship winning its bowl in 2005, and Florida and LSU blowing out their opponents in the BCS and sugal bowls in 2006. Georgia was SEC champion and went to the Sugar Bowl in 2002 and 2005, where they were 1-1. So, overall, the SEC is 5-1 in the BCS Series bowls in the last 5 years. If they somehow have a losing bowl record overall, I guess that just means the Tennessee's and the like are losing when they get to minor bowls. It is clear that the SEC has dominated when they have appeared in BCS bowls, as their only loss in the last 5 years was 26-23 WV over Georgia in 2005.