Okay, now you're just nitpicking.
No, they weren't right at all, quit over analyzing.
I understand what you're trying to say. Do you understand why I think you're wrong?
No, it couldn't be used as a rationale; Jews are mistrusted because of age-old biases towards them; they are considered a threat when in reality they are not. The assassination may have been caused by a Jew, but all it did was stir up the hatred that was already there.
Mutants, on the other hand, are persecuted because many of them go on rampages or fight amongst each other and cause massive property damage. All of the time. See, that's the key difference here; all real-world minorities are just ordinary people going about their lives; they may have different skin color or different beliefs or preferences, but it's not hurting anyone. Mutants are NOT ordinary people, super-powers are not ordinary, and many of them CAN and do hurt lots of people, sometimes without even meaning to.
If ordinary people out on the street were to spontaneously gain super-powers, I would be terrified, because most ordinary people would not suddenly decide to put on a cape and fight crime; they would use their powers to further their own ends. And if they proved to be to much for the law or even the army to handle? Us ordinary people would be screwed.
That said, there are plenty of other mutants that just look strange, and I would love to have a story arc where someone sits down with Charles Xavier and tells him, "I realize that you're worried about mutants being persecuted, and while do you are right to do so, you have to understand that there are mutants out there that really are a threat to the world at large," and the two sides coming together for a compromise, rather than the usual, "all mutants are plotting to kill us and God hates them an we must KEEEEEEEELL DEM ALL!"