Supposed to? Human polls, like the AP & coach's, are on the face subjective which of course introduces all sorts of logical shortcomings. That Bama is pretty much a unanimous #1 despite having a weaker SOS then other undefeated teams is but one example of how wishy/washy ambiguous a system of determining the college football champion the BCS is. If Boise St. had played Bama's exact same schedule this season producing similar results, they'd be like #8. Heck, for the coaches poll it's been revealed a few times where the coach has some person from his staff/office fill out their ballot as they've next to no idea whats going on with other Saturday games. Why should they? They're focused almost exclusively on their team and the next opponent and have no time to spend on things so peripheral. next year's changes won't make things perfect, but they'll be a step in the right direction. Whatever system is finally settled on is likely to be unfair in some way though STOMP
There really isn't a perfect system. At least with a playoff we'll have 4 slots to get a chance at the natty instead of just 2.