I see a lot of peeps approaching this topic from the angle of right vs wrong, good vs evil. It's not that cut and dry. Remember what Magneto says in "First class";
"I have been at the mercy of men just following orders....never again...."
~Magneto
Now not everyone here is going to understand this, but when all power over your own life is stripped from you at that young of an age, it can seed you with a special kind of rage that never really goes away. It won't happen every time, with every person, but when it does happen it leaves you with a kind of smoldering anger, a 'caged beast' if you will. It's always there, lurking, watching, waiting for someone to try controlling your life again, and when they do it tends to pounce.
But what about when no one is doing anything to you and you have to get along in normal society? Where does all that energy go? The answer is nowhere, that's why the scene with Charles teaching Magneto how to focus is so powerful. Magneto has been attempting to control his rage by channeling it into the goal of killing the man who caused the suffering that left him with the rage in the first place. In that scene Charles teaches Magneto how to find peace, how to sooth his rage and channel it effectively. That scene is the scene when Magneto gains the capacity for good where he had none before. However this does not heal Magneto's emotional scarring, and that is what continues to motivate him to evil.
Magneto then starts on the path of killing his oppressors, or 'standing up' to his bullies. Magneto does not view these actions as 'evil' or 'excessive' he views them as necessary to secure the future of himself and others like him. Basically, Magneto is so afraid of the humans that he doesn't feel like he can trust them to be alive. Like a bully who keeps pummeling you and all your friends whenever you turn your backs; do you flinch every time you turn arond and run down the hall, rather than walk, so you don't get hurt? Or do you finally snap, beat the bully unconscious and tell your friends it's ok to come out? So comparing Magneto to Hitler is tempting, but ultimately doesn't hold up as Magneto actually was/is oppressed by humans, since childhood. Does that make what he does right? No, of course not. But Magneto, as a character, makes more sense when we know that.
So that said, I identify with Magneto's pain and mindset far more strongly than I do with Charles's, but I agree with Charles's methods more. The violence has to stop somewhere.
"Be the change you want to see in the world"
~Ghandi