Computers are man made. So are the formulas and algorithms that computers use to rank teams. If those programs were used, people would be complaining that it's inherently biased for/against certain situations. And there'd be no recourse during that season. That's a fallible system, as well.
Let's think of it this way, to put it into perspective ... take something like ESPN's FPI ... we're currently 9th in that ... you're OK with that? We'd be a 10 seed, making way for the ACC champ. If a few things had gone differently for other teams (not having anything to do with us), there would have been potential for us to NOT make the playoff at all this year ... with the same record we have now. Are you fine with that? "Oh, it's just an unbiased computer program ... oh well"?
There's no perfect system. Someone will feel they're short-changed, no matter what.
This is why the only "real" solution is to have everyone in a conference play each other during the season, and only conference winners advance. It's all settled on the field. The least amount of whining possible, there. You'll still have people complaining about that Conference X is tougher, or Conference Y is easier, but everything is still based only on what happens on the field of play, against teams playing the same comp as you.