It was, what, 4th and 2?
I wouldn't have questioned a punt. It's an unwritten rule of football back to the dark ages that the failure to punt on fourth down is a leading cause of losing. That would certainly apply here. That said, on 4th and 2, I would have at least CONSIDERED running load option, perhaps out of Power I. Keep the guard in to seal the line, and the power back and fullback take out the end and Sam backer, allowing either the QB or the TB to get the first down.
I believe that such a play call would have worked. But even with that, the punt would have been the better call. Pin the Dolts deep. Who knows? Brady may have been picked on the following first down. Barring an interception on a fly pattern, any pick would have cost NE more in yardage than a punt.