Most churches in America have organized as "501c3 tax-exempt religious organizations." This is a fairly recent trend that has only been going on for about fifty years. Churches were only added to section 501c3 of the tax code in 1954. We can thank Sen. Lyndon B. Johnson for that. Johnson was no ally of the church. As part of his political agenda, Johnson had it in mind to silence the church and eliminate the significant influence the church had always had on shaping "public policy."
Although Johnson proffered this as a "favor" to churches, the favor also came with strings attached (more like shackles). One need not look far to see the devastating effects 501c3 acceptance has had to the church, and the consequent restrictions placed upon any 501c3 church. 501c3 churches are prohibited from addressing, in any tangible way, the vital issues of the day.
For a 501c3 church to openly speak out, or organize in opposition to, anything that the government declares "legal," even if it is immoral (e.g. abortion, homosexuality, etc.), that church will jeopardize its tax exempt status. The 501c3 has had a "chilling effect" upon the free speech rights of the church. LBJ was a shrewd and cunning politician who seemed to well-appreciate how easily many of the clergy would sell out.
Did the church ever need to seek permission from the government to be exempt from taxes? Were churches prior to 1954 taxable? No, churches have never been taxable. To be taxable a church would first need to be under the jurisdiction, and therefore under the taxing authority, of the government. The First Amendment clearly places the church outside the jurisdiction of the civil government: "Congress shall make NO LAW respecting an establishment of religion, nor prohibiting the free exercise thereof."
Religion cannot be free if you have to pay the government, through taxation, to exercise it. Since churches aren't taxable in the first place, why do so many of them go to the IRS and seek permission to be tax-exempt? It occurs out of:
Ignorance ("We didn't know any better")Bandwagon logic ("Everyone else is doing it")Professional advice (many attorneys and CPAs recommend it)