The only reason why Bill went for it b/c he knew his defence couldn't rush Peyone nor cover his receivers hence the drive that cut the lead to 6 that took less than 2 minutes and thus if you punt he has another 2 minutes to drive them to win the game. If the Pat's could have made Indy take longer to score to cut the lead to 34-28 then the decision would have been different but when you have guys who cant rush the passer and guys in the secondary who can't cover then it adds up to a Colts win regardless of where Peyton starts on offense e.g. Pats 30 or Colts 30.
This is a costly loss that not only cost them a chance a 1 seed but probably a 2 seed and when the Pats don't get a bye they don't come out of the AFC e.g. 05 & 06.