My beef with religion is the way it is so often used to stand in the way of social and scientific progress.
Personal religion therefore, I have almost no problem with. Its usually the large organised and conservative religious groups that irk me, like the Catholic church with its beliefs on homosexuality and abortion (for example that poor nine year old girl that conceived twins from being raped and the church excommunicated her mother and doctors for aborting them =/) or half of the backwards and twisted beliefs of conservative Islam (for a culture that was so far ahead of the west a thousand years ago, how can they be so far behind now?).
I honestly believe that in modern civilisation organized religion causes more problems than it solves, it was necessary in the past as a societal glue and a control mechanism however the need for such a thing is long past and human society will hopefully (and logically should) evolve out of it.
