Computers don't have the ability to take mitigating factors in. The BCS forced them to take out margin of victory to avoid teams running up the score, and even if you allowed it, it's hard to tell apart a garbage TD you score in the 4th vs. a legitimate blowout but with a meaningless TD given up in the last seconds. And without it, if the obviously best team in the country wins in a bunch of blowouts, but loses one game due to terrible weather, terrible calls, and injuries that knock out their top 2 QBs they may be behind a team that gets blown out once and lucks out a win every other game.
Injuries, luck etc. shouldn't be taken into account. They are part of the game. To illustrate the point, let's take it to the extreme, and say that our 10 best players all go down with serious injuries right before the season starts. They are all out the first half of the season, and we lose four games without them. They then come back and we finish the season 5-1, finishing 8-5. Even though we are clearly a great team with everyone healthy, what matters is what actually occurred on the field. Injuries, weather, or luck should make no difference in determining the highest rank team. So let's say some other team-- we'll say Arkansas-- gets
tons of lucky breaks, and even though they are clearly inferior talent-wise, their incredibly lucky season ends up 11-1. Even if Nebraska is the better team, Arkansas produced the far more deserving results, and thus should be ranked well ahead.
Always keep in mind that rankings, when determining the national champion, are in place to find the most
deserving team based on the results on the field, not the
most talented team. If it was the other way around, there would be no reason to play any games. We would simply have a team of skilled talent scouts watch every team practice for a couple months, then declare the most talented team (probably USC) and crown them champions. The fact that many things (injuries, luck, weather, bye weeks, home field, off-the-field distractions, etc.) factor into the outcome of any given game, and the superior team talent-wise can still come out on the losing end, is a huge part of what makes football (or any other sport) so great.