ND went undefeated when no one else did including wins against, prior to the bowls, #11 Oklahoma, #6 Stanford, and #18 Michigan. Yes - they should have lost to Pittsburgh, and perhaps Purdue. Yes - Taylor did get in the endzone in OT despite what the officials wrongly ruled. But they won those games and deserved to be in the NC game this year.
But don't worry. In 2014 we will get a 4-team playoff and it has already been announced that there will be no limit to the number of teams from a particular conference in the new four-team playoff format.