Where libertarians and conservatives disagree primarily is that libertarians believe that virtually nothing can be done by the state without harming someone directly or indirectly. Libertarians tend to oppose almost all zoning regulations for example. Libertarians want a 100% secular state, but one that places no restriction on freedom of religion. I am mostly a libertarian so on that I can say that we do not support any taxation period on churches and any business they run should be treated like any other business. We have no problems with non-coercive public prayers including students praying privately in classrooms so long as the teacher does not initiate it because that scares the other students into thinking that if they don't join in their grades will be affected. After school, let the teacher direct prayers with willing students as long as they and the parents want to.
The personal freedom area we differ the most is that we place virtually no value on "morality" that exists only because of a coercive state. For example banning Cradle of Filth's music is pointless, it is an intrusion into their right to freely express himself and it won't make their followers moral. They have chosen to be immoral and their choice of music reflects that. In case you are wondering, CoF is a blatantly satanic rock band. It doesn't sing about depravity like Manson does (IIRC he is an atheist, not satanist) they glorify satanism in their music. Essentially where we differ is that we realize that coercion alone is incapable of changing them. You can put a gun to their heads and they will only "give it up" in order to not be killed, but their minds won't have changed for the better. In fact you will probably have made them more determined in their belief that they are right and you are wrong.