In this fictional world...in which the movie will be set...Mutants (be they Black, White, Asian, Gay, Trans etc.) are the minority. I think that very basic understanding of the premise is lost on many readers in this "enlightened" present in which we are living.
Scott is no less hated and feared than Storm who is no less hated and feared than Mystique. They are ALL equally hated and feared and persecuted...for being Mutants.