How much more political tension and upheaval do you want? 

If you assess property taxes on churches, you then have to let them be able to protest their taxes every year. How do you tax churches, by number in each denomination or by size/amenity of each church? 

OK, let's say you do figure out how to tax churches. Where I live, and I know it happens in other places, big-box stores annually protest their property tax bill just because they don't want to pay that amount. Most of the time, that is settled out of the protest procedure. So if churches get taxed, you have to let them be able to dispute their amount. Then say they settle out of the system, too. But, for example, you have the Catholics getting a better deal than the United Methodists. So does that show the government favors one denomination over another? Gasp! So would taxing churches mean you have to rewrite the Constitution?