The reason the government does not tax the church is because, at an earlier time, people understood that the church was not under the authority of the government, ....while you individually are, the church is not....but alas that was a long time ago before we began to see everything/one as an entity subservient to government.
If the Church were spending the revenue it does not pay in taxes to help God's Children, that would be a good reason to keep the exemption. When the Church is spending the money creating political uproar, encouraging people to march in the streets demanding that the Government "Feed My Sheep" (not at all what Jesus commanded), buying up prime real estate and traveling the world to conferences denouncing Israel, I think it becomes harder to justify letting them have a free ride.
Remember the saying "He no play-a da game, he no make-a da rules"? If the Church won't join the community in carrying the taxation cross, why should it be allowed to sit back in air conditioned comfort and demand that the proletariat carry that cross?