First of all, the score was tied when Brady came out, and I'm inclined to say that the big return (with no penalty, oddly enough, despite the block in the back many people saw) and the very generous spot to Evans on the drive had a lot to do with that. Miami lost a touchdown due to a weak holding penalty. There was a very strange holding penalty called in the final minute - not strange that it was called, but strange that it was enforced from the end of the play. It's extremely rare to see an offensive holding penalty enforced from the end of the play. This means the foul occurred at the end of the play, which is odd. It helped that the Patriots effectively went from 3rd and long to 3rd and 1. Then there was the roughing the passer penalty, which was also pretty weak.
The refs helped the Patriots out. They lost anyway. I don't really give a damn who's playing or not. It's a cop out to make a claim like "the Patriots would've won if they had to." I don't care if they line up Bert & Ernie behind center, if they lose, they lose.