This hadn't occurred to me before, but imagine a town where the government is hostile to Christianity (or any religion that enjoys exemption from property taxes). What's to prevent them from deciding that, in the name of economic development, a church's land should be seized and turned over to a shopping center developer? I'm not aware of any provision of the law or of the Supreme Court's Kelo reasoning that would prevent such a seizure.
But hostility to religion is not necessary to such a scenario. It's no secret that many cities resent the fact that churches take up so much prime city-center real estate. Wouldn't it be great (in the eyes of city officials) if these properties instead were owned by persons or corporations who would benefit the "public good" by paying taxes on said properties?
Yogita Patel explores this issue in Christianity Today.