Churches are currently exempt from taxes since they're listed as non-profit organizations, in spite of separation of church and state.
However, most if not all churches influence the way American citizens vote. Also, a megachurch profits(on average) about $6.5 million per year. An estimated $71 billion per year is lost in US tax revenue because of religious tax exemption. If taxed, the national debt would be paid off.
Church institutions are politically affiliated, as well as businesses. They should not be tax exempt.