He fights for America... sort of
Connor's alliance in the Revolutionary War is clear: he fights on the side of the red, white, and blue (yes, we know those are the Union Jack colors, shh). In every video we've seen he's chased down and killed British Templar, and we've already heard that he's going to be working alongside the founding fathers. That said, we don't know if he's doing it for patriotic reasons, or if his actual motives are more in line with those of the Assassins'.
It makes sense, too, that the settlers would be Assassins. Assassin's Creed: Discovery explained that the Assassins knew of an Apple of Eden in North America, so it fits that it would have gotten to the continent first, only to be followed by Templars trying to take it back.