Really?
In AC1 the trailers showed Altair going after Crusaders for the most part, yet both the Saracens and Crusaders were enemies of the Assassins. And though it wasn't made clear until the second game, the Templars were just the continuation of an order established well before the Crusades, well before human civilization in fact.
In Ezio's story arc (I haven't played Revelations yet so I'm unsure of how the Byzantines fit in), it is shown that the church wasn't dominated by the Templars at the beginning; Rodrigo Borgia's rise to power mirrored Ezios, and it wasn't until Brotherhood that the Church was fully a tool of the templars. Even then, there were members of the Church who didn't want to play along, but weren't in a position to do much without getting disappeared. Indeed it's implied that many of the Borgia's poisonings (which did happen in RL) were against priests who wouldn't fall in line. Yes, almost everyone you fight is allied with the Church, but not everyone in the Church is allied with the Borgia. Again, you can't really see this in the trailers.
So I'm not expecting a "'Murica, Fuck Yeah!" storyline. In fact, the trailers themselves contain lines like "They talk of freedom, but for who?" that, if one is paying attention, specifically state that Connor does not fully trust the Continentals. The Templars would obviously benefit from having members in key positions in the resistance and in the various governments of the Colonies and later the United States. Yes there's a bias in the most recent trailer, but what else did you expect on July 4th?
There are good reasons to be disgusted with Assassin's Creed, but they have more to do with bad gameplay design than their approach to history. I've described AC as the action games Neil Stephenson would probably make, and though he's now making an action game and it's not like AC, I still think it's a good description.