One of the great things about the Xmen movies is that you can see both of their points of view.  Xavier wants a peaceful solution, and is somewhat naive about it, and Magneto, having already been through a similar situation, sees what could happen and wants to stop it by force.

Honestly, if I was in that world and a mutant, I don't think I could join either, though I might work at the school to try and help the kids.