the thing about Magneto is that he's willing to harm or even kill people to accomplish his goals.
that's why the conflict is so classic, it dates back to Shakespeare, the Realist (Magneto) vs the Idealist (Xavier).
Magneto has that helmet, so Xavier can't touch him. even if he could, he wouldn't kill Erik unless he REALLY REALLY needed to (and even then, there's a good chance he wouldn't)
Magneto manipulates metal, so Wolverine can't touch him.
going back to the helmet, this means NO telepath can touch him.
not to mention, you can't shoot him, he'll just stop the bullets.
the thing that makes Magneto such a great villain is that he is basically the same as Charles, only he's willing to resort to violence.
but Magneto's not the ultimate threat in the Marvel Universe, or even the X-Men movie universe. in the comics, I'd say Galactus, Loki, and Mephisto are greater threats than Magneto. and even in the movies, Deadpool (oh, excuse me, I mean, WEAPON XII... seriously, the FUCK were they thinking?), Phoenix, and Wolverine are more powerful.
Magneto is proof that brute force isn't required for a great villain. it's like Ozymandias in Watchmen.