I would not prohibit religion. However, I would tax them the same as any other organization, and not allow them any special privileges or exemptions from following the law. I would also require that everyone attend public schools, in which science, logic, and philosophy, among other things, would be taught from an early age.
"A wise man ... proportions his belief to the evidence."
— David Hume, An Enquiry Concerning Human Understanding, Section X, Part I.