There have been few legal controversies in the late Twentieth Century which have changed the American political landscape as the controversy between the IRS and Bob Jones University. Is the concern over what happened to Bob Jones University in the 1980's part of what is driving the current religious activism against SSM, because of Catholic Colleges and BYU?
There is a constitutional right to not being discriminated against. There is not a constitutional right for anyone, even churches, to receive tax exemptions. Tax exemptions are at the whim of the government. The government has outlined on what conditions it will allow tax exemptions. Organizations can choose to conform to those conditions or can choose not to. No one's constitutional rights to practice their religion or their rights of free speech are in jeopardy. Bob Jones had a choice to