In my prior post, I reference this article.
Except for churches, their integrated auxiliaries, and public charities whose annual gross receipts are normally less than $5,000, organizations will not be treated as described in section 501(c)(3) unless they notify the IRS that they are applying for recognition of section 501(c)(3) status.
If you are 501c3, you are subject to government oversight, which is what you agree to. You are putting the goverment above God, essentially. If you're 501c3, you cannot speak for or against a government candidate or agency. You become "open to the public," which means you risk compromising your beliefs.
I would also suggest reading here and here.
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...