There was a time when churches provided social services to those they served. Churches ran schools, hospitals, orphanages, and soup kitchens. Though these organizations were not completely apolitical, they were principally charitable to the benefit of society. Since government did not provide these services, it may have made some sense to exempt these organizations from taxes.
Today, churches are among some of the most profitable businesses. They engage in less activity that is of benefit to communities and more activity that is directly and overtly political. They do not deserve tax exempt status.
Wealthy Americans hide vast sums from appropriate taxation by funneling monies through religious bodies. Churches use the money to support candidates and provide benefits directly to donors.