has a very long history in Western Civilization. That is because the Christian West thought more christian-ly than we do now.
Some background....In the days of the Roman Empire they believed that the emperor was divine, a god, which gave him all power over every aspect of life. As god, the emperor could tax and control whatever he wanted. He was it; the government was it.
Over the course of a few generations Christianity "turned the world upside down." People began to understand that the emperor/ government was not god, after all, which over time naturally curbed the government's power. The idea of "sphere sovereignty" began emerging. That means that the government, the Church, and the family each had its own areas of sovereignty. The government could not control the Church through taxation! We today all know that taxation is a form of control.
The American Founding Fathers understood the Christian concept of sphere sovereignty, and also knew that taxation was a means of control. This is where our tradition of not taxing the Church came from.
That is our heritage, but we have rejected it for the ancient pagan notion of the state as god, which necessarily carries with it state tyranny. If the state, which includes demos (The People), is the zenith of power on earth, if there is no power that exceeds it, then it is god and can tax whatever it wants.
One last comment: churches are tax immune, not tax exempt.