You know, regarding the mob scene in this issue of the X-Men, you kind of realize Xavier is very much responsible for all this crap.
Think of it - we got humans born with strange powers. being kids, they're afraid of standing out, consider themselves freaks, and do their best to appear completely normal. Enter an authority figure who essentially tells them that yes, they ARE freaks, and must absolutely hide these abnormalities from people, because revealing them will be disastrous. He will train them to use these freakish powers to aid humanity, all right, but they must never forget, they must not reveal who they are, or they will never get peace, but be punished like the freaks they are. If they are to walk among normal people, they must hide the fact that they're different.
Xavier then keeps the group in hiding, never making them go public or otherwise make people understand. Then comes Magneto and company, presenting themselves as the leader of these freaks, giving them a label as "Homo Superior", and announcing that they want to take over Earth and rule over the lesser Homo Sapien.
Xavier's X-men group may appear and temporarily halt Magnto's plans, but they don't present themselves as mutants, they don't go public and denounce Magneto's activities, point him out as the terrorist he is, or acknowledge the fact that he's not speaking on behalf of all Homo Superior. They just show up, stop his plans, and go back in hiding, leaving the public confused as to what happened, but completely aware that there are some freak offsprings of the human race that are planning on world domination.

Seriously, you can't blame the humans at all for being "suspicious". Xavier and his "let's keep you freaks in hiding" doctrine left Magneto completely in power to influence people's view on mutants, and even after all the stuff that's happened, and all the attacks evil mutants have pulled, there has yet to be a single "good" mutant to go public and try to inform people that they're not ALL enemies of humanity.

Out yonder, under the shining vault, among men the saying goes: 'Man, be thyself!'
At home here with us, 'mid the tribe of the trolls, the saying goes: 'Troll, to thyself be-enough!'