The whole 'prejudice against mutants with powers' thing has been done to death, most notably with X-men. However, I always felt that it was too over the top, the blind hate being excessive and no attempt was made to justify it. The point is sort of lost if the ones who are bigoted are so over the top villains that everyone can say "well, I'm not that evil, so guess I'm fine."
If someone was trying to write a story that used prejudice, but not in an anvilicious manner, I'm wondering what are more reasonable way those who had anti-mutant prejudice would be like.
What forms of prejudice would occur, and more importantly how would those who were prejudice justify them? My belief is that plenty will hate the unknown, but will try to cover their bigotry with all kinds of rationalizations. Most bigotry of today has these rationalizations, ones that are blatantly flawed and just excuses to hate; but still have some tiny kernel of truth that is simply misrepresented in insane ways to justify bigotry.
Today people try claim come minority is 'stupid' because they have less education on average (ignoring that this is due to difficulty of someone from lower socioeconomic standing getting into, and paying for, colleges) or how illegal immigrants are destroying America by not paying taxes (which ignores the fact that illegal immigrants are a tiny fraction of our population and frankly there are not enough to have a significant impact on our economy no matter what their doing), or that all Muslims are terrorist or untrustworthy by pointing to the actions of a tiny group while ignoring that 99.95% of Muslims do not agree with or approve of the group. I'm looking for these sort of flaws rationalizations people would use to 'prove' their bigotry is justified.
For example assume a world where people develop powers, usually around puberty. Some may look different (think Beast from x-men), others may look like normal humans, and those that look different may or may not gain any power (may in fact have only disadvantages from the changed form).
Also presume that the government is reasonable enough to document special powers and register potential lethal powers. Few powers are much more lethal then having a gun, and many aren't lethal at all. People often use their powers as source of employment, people teleport themselves and another as human taxis, weak healing gifts used at hospitals to patch wounds etc. Powers are rare, but not unheard of.
Also, what will be the thoughts of the err..subtly bigoted. Not the ones that put on white robes to burn effigies or stand outside of funerals with colorful signs about how God hates everyone, but the ones who are mostly decent folk and don't have a desire to hurt mutants, but still have some subtler distrust or unease about mutants.
I already know pretty well the religious argument, and the "they're dangerous" argument; as these are the most common ones used in fiction. I'm more interested in the other arguments that might be made. What would an atheist use as a justification to distrust a group of mutants who are certified as not having 'weapons grade' powers?