I didn't bother reading to find out if this was brought up, but here's the quick and simple. Magneto controls magnetic energy in a stronger sense than the magnets you're thinking of. First off, he controls all metals, second, he is more than capable of putting up forcefields to protect himself (you see him casually holding off Cyclopse's blasts all the furking time), and third, he senses metal. I mean everywhere.
Recently in the comics Magneto tried proving himself worthy of the X-men (because mutants were recently decimated and they have to stick together) by saving Kitty Pryde, who had, in a previous story, saved the earth by phasing a planet cracking bullet through the planet while inside. Before anyone asks, these make sense in context. He sensed that bullet, after years of it travelling through space at a speed that would make the Flash god "Dayam!" and brought it back just as fast.
Add to that the fact that he's a known mutant terrorist, a holocaust survivor, and has had experience in the field and with paranoia for years, he could tell when someone's aiming a sniper at him and crack the guy's skull with said bullet before the man had finished aiming. You don't fight the X-men with just controlling metals, you fight the X-men by being the most badass and powerful mother furker to walk the earth.
