The flip side is that, on numerous occasions, the wild card team has been better than at least 1 division winner in the league. If you view it as a counterbalance for an unbalanced schedule that allows mediocre division winners to beat up on terrible teams, it makes some sense not to penalize the wild card winner.
Not that I have issue with the current format, but it's always felt a little artificial to me - trying to force a dramatic finish that only happened rarely in the previous system. Yes, the Angels had a more meaningful September than expected, but that wasn't a function of their level of play, which has been narrowly orbiting .500 all season. It was more that everyone else was just so bad that they fell away from the pack, and the Twins weren't good enough to really run away with it. It's probably working in the NL, though.