Discrimination Against Religion, and the "Churches Are Tax-Exempt" Red Herring
Tax exemptions are an argument for treating churches like other tax-exempt nonprofits, not for specially excluding them from benefits available to such nonprofits.
In yesterday's Discrimination Against Religion thread, a couple of commenters argued that churches should indeed be denied various benefits—such as historical preservation funds—because churches don't pay taxes.
Churches, though, generally get the same sorts of tax exemptions as do other nonprofits. Universities, schools, museums, concert halls, advocacy groups (except those branches of advocacy groups that participate in electoral campaigns or do a substantial amount of lobbying), hospitals, soup kitchens, and so on all get tax-exempt status. All these nonprofits don't pay income taxes, they generally don't pay property taxes, and their donors get to deduct the donations from their own taxes.
Churches do get slightly preferential treatment in certain circumstances (and I generally oppose such preferential treatment). But the bulk of the tax treatment that they get is the same treatment that's given to other nonprofits.
So if you think that all tax-exempts nonprofits should be denied, say, historical preservation subsidies, that would make sense. Or if you think that the subsidies shouldn't exist at all, that too would make sense.
But if you think that historically significant museums, opera houses, university buildings, and the like should get preservation subsidies, despite being tax-exempt, then I can't see how the tax-exempt status of churches should somehow exclude them from the same sort of subsidies.