What's the argument against taxing churches? Is it the idea of separation of church and state? That churches should exist independent of governments? Because when done honestly I support this idea.

On the side of wanting taxation we see scams like Mega-Churches in the US and scammers like Pat Robertson "preaching" about how he needs a private jet to spread the word of God, you know the typical exploitative and frankly sinful scams televangelists using religion to make money tax free by exploiting the gullible.