The pats were scoring a lot, but remember one of the TDs was a pick 6, and the poor Indy special teams kept resulting in great starting field position for the pats. I think Indy's D did very well after a shaky start.
The Pats got 319 total yards of offense averaging 5.4 yards per play. What killed them was the defense's complete inability to get off the field, as demonstrated by the Colts 80 total plays compared to the Pats 59.