In a few hours I'll agree with you that Patriots was the better team, especially in the first half.
And yes, it's by no means certain they would gotten a TD on the drive regardless of whether they would have been called or not.
I think I'm just disappointed by Colts, and especially Mannings, play today, much like when Atlanta Falcons surprisingly went to the Superbowl, and then played their worst game of the season. That was Colts today, their worst performance of the season.
But in real football (soccer) we have a saying that goes something like this: "You're only as good as the opponent allows you to be". So in that light it was a deserved win for the Patriots.