Evolutionary Path
This is a rather surprising article from The New Republic about the social implications to be found in comparing the movie X2 to the current versions of the X-Men comic books (New X-Men by Grant Morrison & Ultimate X-Men by Mark Millar, among my own personal favorites). In it, the author notes that "X-Men" has always been an allegory for the relationship of minority communities with the majority culture, where Xavier represents integration and Magneto represents violent separatism. But the author laments that, unlike the film, the current comics paint Magneto's POV in a much more fashionable light.

Point taken, but I think the comic writers are less interested in espousing a militant agenda and much more concerned with injecting some emotional realism to these stories. Yes, Xavier is a proponent of integration, but, after literally thousands of stories where various regular humans have tried to commit mutant genocide, some of which include several glimpses into possible future timelines where mutants are enslaved by the majority population, I think any sane man would begin to doubt the viability of peace. The problem, ultimately, with Magneto's view is that it's much easier to maintain in the face of adversity than the view of peace. Just look at the Middle East.