In the past, the IRS has investigated churches that it suspected of violating the Johnson Amendment.

Four days before the 1992 presidential election, the Landmark Church in Binghamton, New York, ran a full-page ad in USA Today that said, "Christians Beware," followed by a list of Bill Clinton's positions on homosexuality, abortion and the distribution of condoms. At the bottom, the church asked for donations to help pay for the ad.

According to Lynn, Americans United filed a complaint, and the church lost its tax-exempt status in 1995.

Landmark Church pastor Dan Little took the IRS to court, arguing the agency was violating the church's First Amendment rights and the agency was only able to revoke the tax-exempt status of a "religious organization," not an actual church.

Both a U.S. District Court judge and a federal appeals court rejected those arguments.

Johnson, the Indiana pastor, laughs when asked about those who question whether a pastor should be allowed to endorse from the pulpit.

"Pastors understand the so-called separation of church and state, as it is currently understood. We understand how marginalized we are becoming," Johnson said. "We are supposed to be part of the community discussion about issues that matter."