Part of the point of the parallels made between mutants and jews is that hiding doesn't work, and that you'll be found-as seen when the school is attacked in one of the previous movies. Unfortunately things don't really calm down as charles wishes they will. Magneto sees that.

I had someone add to my post about how they didn't understand how Magneto with his experiences would want to subjugate another group of people. They don't understand that he doesnt. He doesn't want them as slaves and he doesn't want to kill the humans. He wants them to see that mutants are powerful and if the humans try to come after them, he will retaliate. He won't stand by and see another generation of his people- jewish or mutant- attacked and registered because they're different. 


[s]That's actually another reason I'm angry Scarlett Witch isn't jewish in the avengers movies, because then it makes a lot more sense as to why she would be on Cap's anti-registration side.[/s]