And that's the problem.
The thing is, there are powerful mutants out their that don't fight for the sake of humanity. There are mutants out there that commonly go on rampages, or use their powers for their own selfish gain. And while they may be in the minority, they do it with alarming regularity. And so it's arguable that normal humans are right to be paranoid about mutants; just because most of them mean no harm to you doesn't mean that none of them won't.