Each year, when the BCS rankings are released, there is some sort of controversy. One team is ranked too high, one team is ranked too low; no matter what, the system always pisses someone off.
The BCS also has certain teams that it seems to favor each year in its rankings. If you are in the SEC, you have a good shot at having a good ranking in the BCS, as the ranking loves the strength of schedule that comes from playing in that conference.
And if you are not in an automatic qualifying conference, don't expect to be ranked near the top with the big boys. The BCS is not a fan of the Boise States and TCUs of the world.