Why should a religious organization get to take advantage of what my taxes pay for? Everything they get, they get by piggybacking on my dollar. I don't consent to that.
Should a pastor pay taxes on his income? (It is not required, though some do.) Is it a hindrance on the free practice of religion if he is required to? What about on his housing allowance? What about on her car allowance?
I think my paying taxes is a hindrance on my free exercise of atheism. (Note for the purposes of interpreting the 1st amendment, SCOTUS has ruled that religious stance -- not being religious -- is protected.)
If a church gets road maintenance, power lines, etc., they should pay taxes. They needn't pay taxes on every facet of their budget, but they should budget for property taxes to cover infrastructure costs.