Well, they get an exception for the simple reason that while Baker's sell cakes and florists sell flowers and government sells a legal system, churches actually DO sell religion, and religion is an oft hateful and bigoted product. It is unable to sell bigotry if it is unable to endorse that bigotry through enforcement within its own walls.
Now, whether they ought get tax exemptions is a whole other story. I wonder if there is enough money in bigotry to also afford a fair share of contribution to the legal system.
Don't get me wrong. I'd have to be in dire straits to work for a 'religious' organisation, and frankly I
would not want the services of any baker or florist who objected to taking my money for my big fat gay wedding.
But I do object to the idea that it's 'okay' to discriminate against me because God told you to be a homophobe, but it's not okay to discriminate against me because you're just a homophobe.
If we are to have a separation of church and state, we can't tax churches.
Taxation is the government's most powerful tool of policy. If you want to make something difficult to do, put a tax on it. If you want to make something easier, give it a tax break. That's the way it works and if we decide churches are now tax worthy, we cannot avoid mixing church and state until there is no separation.
Whatever anyone's opinion about religion, there is no way to justify taxing a church because they disagree with us on a particular issue.
One thing churches discovered a long time ago is, people's opinions, beliefs, and feelings, cannot be legislated. Governments are sometimes slow to get that one.
Government can mandate that all government services are to be administered to all, without regard to race, creed, color, sexual identification, yada, yada, yada. In the present day, this includes all branches of government which spend Federal tax dollars. This immediately incorporates the entire public school system. Federal funds are intrinsic to the operation of the healthcare system, so they are also caught in the net.
What a private individual does is a little different. A cake is not a government service, so it gets a little strange when the government says "You will bake for anyone with the money to buy your cake." To make it stranger, in order to be convicted of a cake violation, the baker must incriminate themselves, and admit they refused to bake because the customer was a member of a legally protected group. The same baker could claim he refused because they were wearing fur and it offended him.
