Rapaire, I'm with you - as an active member of a church, in fact.

I think churches should be taxed like any other organization -- perhaps with the exception of unequivocally charitable programs such as feeding the hungry and clothing those who need clothing, etc. (I.e., church-organized homeless shelters, free community suppers, clothing drives, etc., would not be taxed on the money they bring in or on the properties they use, but buildings and programs that are strictly sectarian in nature -- e.g, worship services in person or on TV -- would be subject to the same sorts of taxes that a political think tank would be.)   

For one thing, I think this sort of policy change would do a lot to encouraging churches to be "conservative" in the use of their funds for things like buildings, decoration, salaries, choirs, etc. -- relying more on volunteers, member contributions, and paid workers who aren't in it for the money.   For another, I think it would make an important distinction between what is widely accepted as "public service" or "humanitarian" work (e.g., feeding people) and things that are much more debatable (e.g., indoctinating people into far less widely accepted dogmatic tenets, such as "the virgin birth" or the belief that "homosexuality is an abomination in the eyes of God.")