Is that a theological question, or a political question? There is only one form of government where they are one in the same.
It is about how the definition of free is getting bounced around.
Anyone who thinks churches need to be authorized by the IRS has no idea what freedom is or what a church is.
And the amendment is even more general....it says that congress can't prohibit my FREE exercise of my religion.
And giving to God is part of my religion.
One other point...some denominations take in a whole lot more money per member than do others. Others, because of their size, simply take in a lot of money.
If the government is in the habit of encouraging good business because it gets considerable revenue from business, do you think it is unusual that corporate welfare seems to favor the really large businesses over the others.
If they start pulling down a bunch of tax money from the ChurchoftheExhuberantGiver, do you think that politicians will be more likely to encourage that religion or to be neutral about it?
What if someone comes along saying, "Don't be any religion at all." Do you think the government will be more likely to look at how much they're collecting from churches and favor them, or do you think that they'll be more likely to say, "We don't care how much money we rake in from religion; We want all you churchgoers to stay home and stop giving."?