Mutants aren't just perceived as a threat, their powers actually are dangerous to everybody around them and the comics have always gone out of their way to show us that humans are entirely justified in fearing them. Beyond that, we've also seen that mutant society has a pretty rigid internal hierarchy, where the "pretty" mutants with potent power sets lord over the ugly and deformed ones, and this is often played for laughs rather than for the extremely troubling eugenicist implications it actually carries.