While the number varies considerably depending on source, the number of Christian denominations is probably at least 30,000, and skisms continue to occur over doctrinal differences. The public shouldn't be required to subsidize every tiny religious fragment. Let the free market weed out failing churches. (One study puts the global denomination count at 45,000: )
Tax credits could be issued for community work and this form of credit could be scaled relative to the communities it served. So low-income churches could avoid any tax burden simply by their nature while the super-rich churches would be encouraged to help out in poorer communities in order to shelter their considerable tax burden.