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> Imagine a government that is very strong on religion A, decides to raise taxes on religion B.

Happens all day long, just a little different and that is by allowing "story A" to be declared a religion, but "story B" not.

In the United States, non-profit organizations are generally tax exempt, whether they are religious or not.

Not in the way churches are.

Generally yes they are. Churches and non profits are generally 501.3.C organizations and share the same tax regulations.

There are, of course different types of non-profit statuses but nothing special available to churches from a tax perspective.