Thanks for such a wonderfully inclusive topic. It surely beat my hands down.
Poly is right. Churches like any other charity - and churches are charities and most do a very good job keeping the taxes down for the state with the programs that they run - are entitled on that basis alone to be tax free.
Churches have costs like any other organization. Yes, some churches are dodgy. They rip millions out of people. Yet churches are not alone in this. There are lots of organization - and this includes public organizations who are corrupt - and which take millions of dollars for themselves and their cronies. Should we simply tax everyone including the government to make sure such corruption is mitigated against?
Finally, people need to be a little bit consistent. Do you believe in the separation of church and state or not? What other organization ought to be separated from the State? Are there others? Separation of church and state is built on the doctrine of separation of powers. Separate powers do not tax each other. Nor do they expect the other to pay them taxes. Can you imagine if the church demanded the State to pay a tithe? It's nonsense.
If people want a separation of church and state then they need to stop demanding the church pay taxes. By demanding taxes, the church thereby is incorporated into the State just like every other legal person. You can't have your cake and eat it. I know some of you think we can. But that is purely nonsensical.
For the record, many organizations such as Kenneth Copeland ought to be shut down as they are corrupt. But so should many political parties. And many schools. And many environmental groups. As well as the nasty gun groups and secret defense programs.