Magneto Was Right
Dude, seriously, Eric Lehnsherr is quite possibly the only comic book villain whose philosophy is superior to his enemies. We all like to believe in the vision of Charles Xavier -- his principles speak to a sense of optimism we would like to nurture and aspire to toward humankind and its potential, and we just plain think it would be cool to live in a world with something as cool as mutants, but without the more uncomfortable "realities" of the X-Men universe -- but human history belies the likelihood of such a utopian future.
Magneto's past as a Holocaust survivor is a lesson that we don't even need as an example of man's capability to give in to prejudice and irrational fear of "the other". History is too full of similar examples to ignore (pogroms, the Red Scare, slavery/Jim Crow/segregation, etc, etc, et-****ing-c). Sure, the Holocaust and assination of Martin Luther King Jr. were effective wake up calls to the evils of prejudice, and Joseph McCarthy's reign of terror came to an end when he went "too far" by targeting the army, but racial tensions and genocides in America and all over the world still exist, as does the fear of socialism, and Jews are far from accepted in many places on Earth.
The end of slavery is a poor example as well of our ability to evolve our social narrative. Even aside from the practical rather than moral motivations of the North to abolish that "peculiar institution" in the South. The practice was only eradicated during the rise of the Industrial Revolution, when slavery was becoming economically obsolete (practicality > morality). One related historical truth that is also glossed over is that when the Spanish began enslaving Native Americans and Africans was that there were intense moral debates over it, which were ultimately decided by practical reasons due to Spain's "need" to compete economically with Britain, Holland, and France. This suggests that human morality is not simply evolving bit by bit, but is perfectly capable in any era of being subverted according to the perceived dictates of pragmatism, only reverting to something resembling "goodness" when events no longer require rationalizations.
But Jews and blacks are potentially a "threat" to white, Christian interests at a far less fundamental level than mutants. How many of you could honestly claim to maintain your beliefs in understanding and inclusiveness when confronted with beings capable of firing lasers from their eyes, stopping time, and even invading your very mind? Such people would be a threat to the safety of both individuals and countries that no real-world race ever could. What's to stop a man who can teleport from infiltrating at will the White House, the Pentagon, the Kremlin, the Headquarters of the UN, or any other parliament or government building in the world? How can you counter a woman capable of controlling the weather from bringing down the wrath of a hurricane, a blizzard, or a flood upon any city on Earth?
Absolutely nothing. Nothing but genocide or the permanent eradication of the mutant gene.
And really, in the face of such threats, would it not in fact be in homo sapiens' best interest to wipe homo superior from the world, or at least to control them genetically and/or legislatively? Would not letting them go unchecked be negligent? No matter how unpalatable such policies and actions would be, might our very survival demand these moral sacrifices? After all, could you continue to support mutant rights after a nuclear strike perpetrated by the Master of Magnetism?
Even if the human race decided for integration rather than conflict, the interbreeding of human and mutant would lead to an ever greater ratio of powered to unpowered individuals, and human history again teaches us that the the powerful will always dominate the powerless. In the interim, racial tensions would still exist, exacerbating resentments between "us" and "them", and embittering mutants against their human counterparts. The growing homo superior population would infiltrate government and the military, making resistance against the eventual mutant revolution impossible as our society would no longer be capable of a unified response. We would become second-class citizens in a de facto mutant tyranny, destined to the same repression we might have inflicted on them in the past, but without the military and technological superiority to counteract their powers (anti-human Sentinels, anyone?).
Magneto is undoubtedly aware of all of this, and therefore has come to the only logical conclusion: get them before they get us. Comic book moral logic may artificially marginalize his beliefs, but in the real world his is the only pragmatic solution.
We may criticize the actions of the PLO, and rightfully so concerning the targeting of civilian targets by individual terrorists, but the practical considerations of the conflict between their greater movement and Israel and the West necessitate unconventional tactics. They cannot meet the superior Israeli military in a pitched battle, so when conventional victory is impossible what else can they do but resort to morally dubious military operations designed to sap their enemies' will to fight?
This is exponentially more true for Magneto and his people. You simply can't segregate mutantkind considering their abilities, and even more importantly that they can be born to any normal humans (regardless of race, creed, or nationality) so any actions by human governments must be proportionally more extreme. It's easy to condemn Magneto's actions as terrorist war crimes, but what is the alternative? Given the stakes, defeat is almost certainly tantamount to extinction, making victory the only option, no matter the cost.
If the only two choices are the death of either human- or mutantkind, what as a mutant would you choose?
Ultimately, the conflict between Xavier and Magneto is one of self-indulgent utopianism vs. realistic practicality, and in a world of realistic practicality, the conclusion is obvious: Magneto was right.
For further reading I would recommend the following sites and comic books (but I'm sure this list is in no way exhaustive given the fifty-year history of the X-Men).
Magneto Was Right - Magneto Was Right: a Magneto fan-site which provides intellectually in-depth articles on Magneto's beliefs and character which are far more exhaustive, insightful, and well-researched than this post.
Highly recommended for comic book fans and students of philosophy and psychology alike.
Magneto: Testament: A comic book mini-series recounting Magneto's history from child- to adulthood under the Nazis and the Holocaust. Possibly the most important and terribly horrific account of the prejudice that mutants would later endure. One particular scene in issue #1 is the entire story of the X-Men distilled in no more than a few pages. Don't read if you like people and wish to continue to do so.
Uncanny X-Men #150 - I, Magneto: The moment when Magneto went from "a poor man's Dr. Doom", spouting cheesy speeches of world domination, to complex, mutants' rights crusader. If you want to know where his modern incarnation and world view were first articulated, then this is the issue you need to read.