The main complaint leveled against the bowl system is that rankings are somehow intrinsically less fair than playoffs. A few simple stats show that, in football at least, this is simply untrue. For the sake of argument, let's assume that a really top-notch NCAA football team wins 60% of its football games against teams of the caliber it would meet in a playoff (this is awfully generous, I should point out, as the real underdog winning percentage in bowl games is roughly 50%). Let's assume as well that in order to win the championship, a team would have to win three playoff games, just as a conference champion with a first round bye in the NFL would. As we all learned as far back as high school, the chances of a team winning all three games to claim the championship are 60% x 60% x 60%, or 21.6%. If we up the odds of winning a game to 70%, the odds of winning out rise to just 34.3%. The reason odds like these are so problematic in football is that the sample size of one game is laughably small. In baseball, basketball, or hockey, where playoffs consist of multi-game series, the odds of the better team prevailing are much greater (though even in these sports it can be hard to predict; does anyone really think the Colorado Rockies and Philadelphia Phillies were the best teams in baseball the last two years?).
Opponents of the bowl system would interject at this point to argument that playoffs allow teams to control their own destiny. This also is patently untrue. The most compelling argument against this notion is that one team alone cannot control the outcome of a game; if that were the case, there would be no point in playing the games in the first place. Besides, in any close football game (as the latter games of a playoff generally would be), it is generally factors well outside a team's influence that give one side an edge. Weather, field conditions, fan presence (even in a "neutral" stadium, one team will have more fans than another, which really can make a difference in football), and, most importantly of all, human error on the part of the referees routinely affect game scores, as anyone who watched the Oregon/Oklahoma game in 2006 could tell you.
So, to return to my original point, college football has two choices for how it could run its postseason. The supposedly "fair" playoff system is in fact governed by chance and the team that is crowned as champion at the end will almost certainly not be the best from the regular season. The BCS, to be sure, has some flaws as well. Most glaringly, there are too many bowls, and the computer rankings determining which teams get to go to the best games are, in a word, terrible. However, the coaches' and sportswriters' polls that are compiled at the end of the bowl season tend to do a good job of reflecting which teams are the best, not based on a handful of single-elimination games at the end of the year, but over the course of the entire season. Which system, then, is really more "unfair" and less likely to crown a "legitimate" champion? It's worth thinking about. If you care about this sort of thing.
N.B. For those of you who don't follow football, I apologize for pretty much everything about this post, and especially for not explaining what exactly I mean by the BCS and the bowl system. The simple truth of the matter is that, love it or hate it, the selection process for college football's postseason is extraordinarily complex, and explaining it would have just about doubled the size of an already-overlong post. Hopefully Wikipedia will suffice on this one.