Making churches tax exempt was well intentioned as a way to sustain the separation of church and state. The tax code specifically states that a church is only tax exempt so long as they stay out of politics. However, in practice, no politician has had the nerve to insist on enforcing that, as they are afraid they would be seen a persecuting religion. If a politician starts to head in the direction of enforcement, the church only needs to make a hefty political donation and the politician is discouraged by his/her peers from doing so.

I am of the opinion that if a church wants to involved themselves in politics and to have a voice in government, then they should be taxed to help pay for the government.

However, whenever churches have gotten involved in government it has in virtually every case resulted in bloodshed. That is why the U.S. has attempted to separate church and state, and codified a tax code which is supposed to discourage churches from getting involved in government.