That list Stringsinger posted is a pretty good set of reasons to at least find ways to limit religion's direct influence in governmental affairs and the educational system. Although, some 'believers' already are reasonable, others very belief system commands them to interfere and try to impose their values on the rest of society!
THIS is the crux of the problem.... now we need to maintain 'freedom OF religion', while allowing those who wish to have 'freedom FROM religion.'
   It will never be easy to juggle those conflicting views.