The major difference I see between Emma and Xavier (or magneto), and I am sure I'm just repeating what people said above, has nothing to do with their end goals. Each is devoted to the survival of their race against the human masses. Its the means by which they go about ensuring their existence. Personally, I prefer pragmatism, but I can completely see where you are coming from Will.
It is almost defeatist to say "they will never stop hating us" or whatever, and a horrible message to send to their students, but given the reality that they live in, skepticism of the human population is probably beneficial, if not idealistic. In a perfect world, yes, Emma's words would be no better than hate-mongering.
While it probably isn't politically correct to assume that we people may be scared or prejudice against mutants, it is completely realistic. I mean, be honest, if you knew for a fact that there were telepaths, people who could READ YOUR MIND, how comfortable would that make you? I will admit to a touch of the paranoia from time to time, but I don't think I'm the only one that would feel violated by even the idea that someone could be rifling through my head...
Originally posted by xmarksthespot
Pshaw. Xavier sent a group of children to an island to their death. He knew the Danger Room had evolved intelligence and yet kept it as a training device. He's most certainly no saint.
Agreed. Xavier has done many things that have caused negative consequences... However, I see Charles more as a tragic hero, whose own downfall is related to a serious flaw in his character. Its really splitting hairs, because most "tragic heroes" could probably fill in as "villains" if they were not the protagonists of the story, and the distinction between him and Emma here sounds way too much like "ends justify the means" for me to make that argument.