If Stan Lee created the X-Men in the 50s, it would be more likely to be considered a metaphor for communism than bigotry and prejudice. Compare the intended feel-good message of "They're people too, they just look a little different" with an alternate, and more cynical "They look just like us, they're here to destroy our way of life and steal our women!"
Mutants in the Marvel Universe are a subspecies of homo sapiens called homo sapiens superior, branching off due to the effects of an extra gene called the X gene which could bestow them with superhuman powers, and sometimes, but not always, an altered physical appearance. Aside from their superhuman abilities, they are identical to normal humans and indeed can even produce viable, fertile offspring together, which may be normal or mutant.
In the early days of Marvel comics, there were only a handful of mutants, but as writers realized "born with a special gene" was a more plausible explanation for superpowers than "bitten by a radioactive spider," the mutant population exploded. The effects of this on the rest of the world were explored in the storyline E is for Extinction in which it was calculated that, due to interbreeding, the normal human population would be for all practical purposes extinct in five generations. However this was in recent years contradicted by House of M which culminated in the Scarlet Witch depopulating the world of most of its mutants by depowering them, and rendering the survivors incapable of producing mutant offspring (however, later one mutant baby was born, opening the possibility for others).
Ignoring the complications introduced by the House of M storyline for a moment, we see that normal humans are in every way just as genetically obsolete as the Neanderthals were thousands of years ago, unable to compete with a growing population of genetically superior people. The reason Marvel's mutants largely fails as a metaphor for prejudice is because they are not simply "different" than normal humans, they are in fact superior, able to do everything a normal human can do and more. They are a competitive threat to normal human genetic lineage, with normal humans holding their only advantage in sheer numbers, an advantage that was, until House of M, rapidly deteriorating.
Which brings us to the competing philosophies of the two most influential mutant leaders, Charles "Professor X" Xavier and Erik "Magneto" Lehnsherr. While Xavier dreams of a future in which humans and mutants can peacefully cohabitate, Lehnsherr's history is colored by his experiences as a Nazi concentration camp survivor and adopts a "kill them before they kill us" approach to the problem. Unfortunately for normal humans, both of these strategies will have the same ultimate result: a world entirely populated by mutants rather than normal humans. If they don't kill us outright, they will simply interbreed with us until there are no normal humans left.
As for the normal humans trapped in the middle of all this, we are left with three options. The two most practical of these are to either willingly interbreed with the mutants, thereby ensuring the survival of our genetic heritage (after a fashion), or kill them all so we can survive as we are. The third option, to segregate the populations to prevent interbreeding, is simply not a workable long-term solution, especially since many humans possess the X gene without any obvious effects, and can at any time produce surprise mutant offspring.
This same argument can be applied to a growing number of fictional superior human subspecies, such as Harry Potter's wizards, who likewise are, due to birthright, able to do anything a normal human can do and more.
The specific phrasing "Magneto was right" comes from Grant Morrison's New X-Men storyline in which Magneto was martyred to the mutant cause when he is killed in an attack on the mutant island-state of Genosha. This high-profile attack on mutantkind solidified his philosophy in the minds of many mutants worldwide, including, at least for a time, some of Xavier's own students. Regardless of implementation, however, by genocide or interbreeding, the crux of his philosophy is unavoidably correct. Xavier's dreams of peaceful co-existence between normal and mutant are unworkable, and destined to end, by peace or violence, in the extinction of the normal human race.