My main problem with religion is ironically not the belief in a Deity (or deities). I can accept that as an allegory, a sort of personification of the system of values said religion upholds.

My main issue is how a lot of people I see that are strongly religious also don't seem to accept the core tenets of the religion in their hearts. As an example, Christianity is a religion that professes love, but many practitioners are quick to hate others, etc.