Sen Grassley of Iowa tried to do this, in particular with televangelist who have become millionaires.   He couldn't get it done and he's a stubborn old *art.   

The assumption, I think, is that church's provide charity help equal to the value that they would have been taxed.    Some church's  spend a high percentage of their donations on charitable work.  Some on the other hand put it into a their building, pastor wages, mega churches with bowling alley's and McDonalds on property.

Tough question.   I think the current tax code is likely being abused far beyond its original intent

My favorite pastor, now in Greeley Co. has been making yearly visits to Peru.  Hell come back and say they established 20 new churches!   What that means in Peru, is 20 homes that have opened themselves to Sunday meetings.   Now that is ground level faith, almost no overhead, no trappings, no expensive media toys.      Oh, and they don't ask for tax breaks.