The refs have been in the bag for the Pats for years. I first noticed this Donte Whitner's rookie year when, after his TD return the refs called a late phantom PI call that the commentators couldn't even guess who the call was against.
The m.o. is almost always the same. The game is called evenly except for a huge break for the Pats early in the game, then one late in the game. They'll often give the Pats a bad break when it doesn't matter (i.e., opponent has 2nd and two from their own 30 yrd line)
This bias is a well known fact - yesterday I was watching the Giants-Chiefs game and the announcers said something along the lines"...there goes Vrabel lobbying the officials for a holding call. Hes not going to get one though, that only works for Patriot players, he's not used to being a Chief yet..."