I don't think every official reffing a pats game has some corrupted conspiracy plan to help them win. Like someone said before, that would have been leaked by now. I wouldn't be surprised if there have been a couple refs in history that had some donaghy-esque gambling problems and tweaked a call here or there in random games.
That said, I do think refs suffer from two different biases that hurt teams like us. One is similar to the NBA, where good players are more likely to get calls. Even if it's subconscious, I'm sure refs benefit them from time to time, which obviously benefits teams like the pats. The other is that I think they make calls to fit the narrative of an exciting game. Case in point, last week's PI call that the pats win the game with (also the non-calls on the Steelers end of game scramble). I think a ref is more likely to make the call that results in a good storyline, even if they don't do so with premeditation. This wouldn't necessarily benefit a better team.