BOTR, as to the FFRF case referred to by Sol Reform, it was out of Wisconsin, which is within the Seventh Circuit. I don't think that's an overly conservative circuit, outside of the well-known free-market judges. I initially wondered about the standing issue, which can be hard to come by if you are just asserting standing as a taxpayer, but after looking at the opinion, that wasn't the basis. The plaintiffs clearly calculated far in advance how to attack this particular statute. People like Marci Hamilton have been saying for a while that the Parsonage exemption is unconstitutional, but obviously striking it down is a small measure in the overall taxing discussion.
As to courts stepping in to eliminate tax exemptions, I think the prevailing view in that niche of the legal community is that it's not constitutionally mandated to either allow or prohibit property or income tax exemptions related to religion, and it should be left to state legislatures, in the case of property taxes, and Congress in the case of income tax exemptions. Aside from Justice Douglas's solo dissent in Walz v. Tax Commission, I don't think anyone in the upper eschelon of the courts has ever taken the position that it's unconstitutional. In fact, I suspect that if one of these laws does ever pass and allows tax breaks for charitable orgs but not churches, some kind of constitutional challenge would be launched by the church community on the basis that it's entanglement to inquire how much social benefit regiously affiliated organizations provide. Burger actually suggested that in Walz. I do think that in the end, if this form of subsidy is to end, it will have to be judicially. It's just too much of a minefield politically. I think it's possible that Douglas's reasoning might be vindicated in the end, and he might end up being 100 years ahead of the bend of history.
I also suspect that state laws on property tax exemptions would be more susceptible to eventual challenge in court than portions of the federal tax code.