The X-Men remain neutral in The Civil War. Well, all except Bishop that is. Which is an interesting twist because he's a soldier from the future where Mutant Registration was forces. His reasons, though, work fairly well.

Without having read House of M, there's a lot missing. The main crisis in this collection is Domino and Shatterstar breaking the 198 (that is those non-X-men mutants that survived the Scarlet Witch. Can't say more, because I've yet to read House of M myself) out of the Xavier Institute where they are being "protected" by man-operated Sentinels. Now the original 4 X-Men (minus Marvel Girl) try to find them before Iron Man and his pro-registration cronies (led by Bishop) do.

So, yeah, seems a little forced. Like, "we're doing an all-Marvel story so we have to use the X-Men but they just went through their own major crisis and so we need to still deal with that" kind of thing. Don't get me wrong, on its own, it was a pretty decent story, I just don't see why it needed to be billed as a Civil War story.