Interesting Time magazine article about this subject
http://time.com/3939143/nows-the-time-to-end-tax-exemptions-for-religious-institutions/
I could be wrong about this, but my understanding is that organizations who classified themselves as religions were exempt from taxes to uphold the church/state notion - you stay out of our business and we'll stay out of yours. The problem is that religion isn't staying out of government business and constantly lobbying to change or influence laws based on religious belief. This sucks (or blows, depending on your perspective) and a change is very much needed.