Why are church's tax exempt?

That was to ensure separation of Church and State. This way no government entity can tell a Church what to do. NY City attempted to force Christian Religions with paid employees to provide Birth Control Prescription Coverage or lose all city contracts. The Churches responded with No and told the city to cancel the contracts. Well the Mayor almost choked when he realized the Churches provided 85% of DayCare, Homeless Shelters, Soup Kitchens, Unwed mother programs, Ged Education, teen centers, Abused women shelters, Counseling for addictions and so on.