Here's how I see it:
1. If the pass is complete for a first down- game over. Patriots win.
2. If the Patriots don't get the first down, there's a greater likelihood that the Colts score quickly and leave time for Brady to work some magic. (It nearly worked out that way when Addai broke that run to the one yard line.)
3. If they punt, there was plenty of time for Manning to get down the field and score, leaving little to no time on the clock. Yeah, there's the whole "not trusting the defense" thing, but let's face it, what coach does trust their defense against Manning in that situation?