The prohibition is relatively recent, dating from the administration of Lyndon Johnson, and the reasoning is that churches should not become thinly veiled tax dodges for political campaigns. The 30 pastors challenging the IRS rule are conservative and endorsed John McCain. It might do well, however, to recall that the IRS has attempted to enforced this rule apparently only once in recent times, and that was against All Saints Episcopal Church in Pasadena because of a sermon by its rector emeritus in 2004 that came close to (but not quite) endorsing John Kerry over George W. Bush.
Ultimately, All Saints won the case and its tax exemption was preserved, but the investigation proved costly for the church in lawyer fees over a two year span. It also should be noted that a number prominent pastors this year have endorsed presidential candidates, but not from their pulpits, for example Kirbyjon Caldwell, who presided at the wedding of President Bush's daughter this summer but who has endorsed Barack Obama.
In his column, Fish notes that the issue is more complex than at first blush:
"Pastors are in the business of preaching; their lectern is a pulpit; and they are expected to exhort their parishioners to act in accordance with religious truths, not simply in the privacy of the home and church, but in the world. If in the judgment of a pastor the imperatives she urges on her flock are likely either to be weakened or made stronger by the election of a particular candidate, is she not obliged to declare herself on what is only superficially a political issue but is really a religious issue? Wouldn’t she be derelict in her duty if she declined to do so on the reasoning (which she would reject) that religious doctrine has no implications for what one does in the public sphere?"
In my own work as Chaplain of the California Senate (the photo in this posting is the chambers of the Senate), the separation of church and state was sometimes questioned. How could we justify taxpayer support for a chaplain in the California Senate? While case law clearly supports such governmental chaplains, the question is legitimate. The California Senate has appointed chaplains since 1896, and those serving have included Christians, Jews and Buddhists. In fact, the federal government has supported chaplains of virtually every faith in the military. As the state Senate chaplain, all of my prayers were interfaith in tone and content, and I never endorsed candidates or took a position on legislation. I also invited guest chaplains, and I received considerable hate mail (from "Christians") when I invited Rajan Zed, a Hindu, to pray in the California Senate. Now that I have left, the Senate, upon my recommendation, appointed Rabbi Mona Alfi as Chaplain, the first non-Christian in many years and only the second woman to serve as Senate chaplain. The issue of government-sponsored chaplains is perhaps a topic for another day here but it should be part of the wider conversation over the boundaries of religion in politics.