Originally Posted by C. Lee
The XMEN are natural genetic mutations that could happen to anyone (you, your brother, your sister, your son, etc...) and people fear that they or someone they love could turn into somekind of monster...and thus hate the idea of mutation, and focus it on the XMEN. Many of the times that the XMEN make the news is when fighting other mutants or the government...so they are percieved as troublemakers.
But even that doesn't make sense. There's good meta humans and bad ones even if they weren't born a mutant. Their physiology is altered to make them a threat so why is one hated and one not? Simple. The X-men weren't created to make sense as much as to make a statement of being against bigotry and intolerance to others that are different. Even that is sort of lost in the current x-men movies and comics.