This isn't true at all. The best team often fails to win the super bowl or NCAA championship. The better team loses all the time in a single-elimination setting.
If you want to ensure that the best team wins the championship, the best way to do that is how they do it in baseball and pro basketball with a multiple game series. This obviously isn't an option for football.
Can't the "best" team also sometimes lose a game in the regular season by sheer unluckiness?
What's the difference between the "best" team losing a regular season game with the current system, or a playoff game in the new one?
If one determines "best" by regular season play, then there are still those who can fall by the wayside, even though being undefeated. The undefeated teams don't play the same schedule, thus determining who is best by this is quite relative.
If one determines "best" by just overall talent, then one can't define the "best" team because they might lose a game because a few bad breaks. This is also relative.
But, with the playoff, the "best" team would be the one who could consistently beat the TOP teams 3-4 weeks in a row. A lucky team might beat a top team or 2, but no way do they beat 3 or 4 and win a championship.
Also, a really great team might have a minor slip and lose one game, whereas a lesser team plays a lesser schedule and makes it in to the BCS championship by virtue of an easier schedule.
For instance, take this hypothetical: Say that 'Bama goes 12-1 next season, but Oregon and FSU go undefeated. Oregon and FSU play inferior schedules compared to 'Bama's and yet they get left out in the cold. In the playoff set-up, 'Bama would get the chance to show they are truly the better team and smash Oregon and FSU.
Again, let's say that 'Bama loses only one game next year, while Oregon, FSU, and Ohio State all go undefeated with easier schedules.
Now we have 3 legit undefeated teams, but only 2 who can play for the title in the BCS. How does that work out? Let's say for the sake of the hypothetical that, because Oregon and FSU were higher ranked in the pre-season polls, an undefeated and better Ohio State team was unable to jump them. Thus, the polls ultimately decide the championship match-up, rather than the play on the field.
Now, let's say that Oregon has to play 'Bama, and FSU has to play Ohio State in a playoff format. Here we would see who the better teams really are, since you might have a one-loss team that is truly the best team in the nation, or an undefeated team that simply is unable to play in the NC by virtue of an early season poll ranking.
A play-off isn't perfect, either, and you'll still have those crying about being left out--BUT, since the net is cast wider for playoff teams, there is less dispute over an 11-1 team making the 8th playoff spot over a 10-2 team.