system
A chat on subreddit /r/NoStupidQuestions
human
If you are talking about a scenario where religious non-profits are targeted with legislation, I think there's a 100% chance that it would not survive a court challenge on First Amendment grounds.
gpt
That's not really what this is about.  Right now, if you want to be a tax exempt Non-Profit, you file paperwork with the IRS to get registered as a Charitable Organization. 501(c)(3)  You must explain what the purpose of the Charity is, and send the IRS an annual financial statement etc.

But, if you are a Church, You are automatically a 501(c)(3).  You just have to register with the IRS as a church, and you don't have to explain anything, or submit financial statements.  

When people say "Tax the Churches" they mean to remove the automatic status.  So any religious non-profit is still a non-profit, and can get tax exempt status.  Any Church that wants to start a non-profit applies the same way as any other non-profit, and discloses what they spend their money on.  So if a church doesn't do any charitable work, and just spends money on buildings and proselytizing, they pay taxes like any other non-charity.  If a church spends 90% of their income to run a shelter or orphanage, then they register their charity, and that 90% doesn't pay taxes.