Know ahead of time that this is a really tough topic for me. But I'm going to try to explain it as clearly as possible, here...
Okay. So, there is this way in which it is difficult for American Jews (and by American Jews, I mean me) to speak critically of Israel, or to hear criticisms, because in the American cultural landscape, even valid criticisms sound like antisemitism. Part of this is a kind of rhetorical move made in some quarters of the Left to say that the Israeli mistreatment of the Palestinians makes them just like the Nazis. It does not. Just because both situations are atrocious does not make them equivalent. And saying it does seems to reveal an underlying current of a suggestion that the Jews, perhaps, got what they deserved (or deserved what they got).
And part of this is another move, largely made on the Right, to say that because the Jews suffered, they have impunity in their own land to "protect it" -- as in, to decide how, and how much, the Palestinians will suffer too. This is less openly antisemitic, perhaps. But it rests on two premises that are no less problematic: 1) that, like the first move, there is some sort of direct connection between the behavior of the Nazis then and the Israelis now, and that (even more offensively) Israelis acting like Nazis is justifiable; and 2) that because of the Holocaust, we are obliged to pat the Israelis on the head like good little children and tell them that their actions are okay because, after all, they have already suffered so much.
I go on about this at such length as a preamble to my point: that in its treatment of Magneto, X-Men: First Class seems to promote both of these positions in a really insidious way.
In Erik's final confrontation with Shaw, and in the events that ensue, the film seems to be making the point that Magneto becomes villainous because, for whatever reason, he has come to agree with the viewpoints of his former Nazi tormentors; and it seems to be making the point that in his own mind, Magneto's disproportionately violent actions are justified because he is merely "protecting himself" from further torment.
The first scene that conveys this, as I said, is Erik's final confrontation with Shaw, the former Nazi doctor who experimented on him in an attempt to bring out his powers. Furious, Erik moves to kill him, when in a final attempt to save his own life, Shaw says something to the effect of: "there is a war coming between the Mutants and the Normals; we mutants are the superior race; and evolution demands that we exterminate the Normals like the vermin that they are, in no small part because they would kill us if given half the chance." Erik immediately agrees with this (clearly Nazi-inspired) position, and in fact agrees so wholeheartedly that once Shaw's speech is done, the only further reason Erik can find to kill him is that "you killed my mother." I recognize that the film must remain within the bounds of what we already know about Magneto's positions. But as I said above of Israel, it draws a false equivalency between (in this case) the "Jewish problem" and the "Mutant problem," the Nazis and the Jews.
The second scene is on the beach, at the end. The combined military might of the American and Soviet navies fire on the Mutants in order to exterminate them. Magneto stops the barrage of missiles and shells, and turns them around. As Charles tries to reason with him and prevent him from destroying the two navies, Magneto cuts him off with a cry of "Never Again!" (the mantra of holocaust survivors) and sends the missiles flying toward the ships. This is, again, I think less obviously antisemitic than the first scene; it seems to portray the empowerment of a disempowered soul. But like the Right-wing defense of Israel, it seems justifiable only if we assert that because Erik suffered a form of genetic cleansing, he has the right to perpetrate genetic cleansing of his own; and that because he suffered, we must forgive him his actions. Magneto, of course, fails to destroy the navies. But it is not for lack of desire. The missiles fall into the sea short of the ships not because he has a change of heart, but because he is distracted by Charles's paralysis. And when, at the end, Erik and Charles divide up the mutants into "teams," Charles seems to think that though Erik's methods are wrong, his overall ideology is basically no less valid than Charles's own.
You can disagree with me if you want. I recognize that the way I've described it here, it sounds an awful lot like I am over-reading a more-or-less vapid movie. But I think it sounds that way more because I have such trouble talking about antisemitism than because I am in fact over-reading. It is there, I tell you. All you have to do is watch.