Lynn and Americans United say that bureaucratic uncertainty as to what level of IRS official can initiate an investigation leads to lack of enforcement.
In the past, the IRS has investigated churches that they suspected of violating the Johnson Amendment.
Four days before the presidential election in 1992, the Landmark Church in Binghamton, New York, ran a full-page ad in USA Today that said, "Christians Beware," and that was followed by a list of 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 in 1995 the church lost its tax-exempt status.
Landmark Church Pastor Dan Little took the IRS to court, arguing that the agency was violating the church's First Amendment rights and that the agency was only able to revoke the tax-exempt status of a "religious organization," not an actual church.
Both a federal judge and an appeals court rejected those arguments.
When asked about people who question whether a pastor should be allowed to endorse from the pulpit, Johnson, the Indiana pastor, laughs.
"Pastors understand how 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."