Call it the metaphysical counterpart to the president’s recent tendency to throw down the gauntlet to conservatives: his National Prayer Breakfast speech yesterday returned to an old theme that absolutely infuriates a certain type of religious conservative, and added to the offense by reminding listeners of Christianity’s past association with holy violence.

The latter drew the most immediate attention, per this report from the Washington Times‘ Dave Boyer:

Speaking at the National Prayer Breakfast in Washington, Mr. Obama said Christians can’t lay claim to a higher moral ground in discussions of how to confront violent extremist groups such as the Islamic State, also known as ISIS or ISIL.

“Unless we get on our high horse and think this is unique to some other place, remember, during the Crusades and the Inquisition, people committed terrible deeds in the name of Christ,” Mr. Obama said. “In our home country, slavery and Jim Crow all too often [were] justified in the name of Christ. It is not unique to one group or one religion. There is a tendency in us, a sinful tendency, that can pervert and distort our faith.”

His comments, in the wake of the president’s much-publicized reluctance to utter the phrase “radical Islam” out of concern that he’ll alienate moderate Muslims, drew angry reactions from some Christians and accusations that Mr. Obama was inadvertently offering justification for Islamist extremists.

Former Virginia Gov. Jim Gilmore said the president’s comments “are the most offensive I’ve ever heard a president make in my lifetime.”

“He has offended every believing Christian in the United States,” said Mr. Gilmore, a Republican. “This goes further to the point that Mr. Obama does not believe in America or the values we all share.

While some of Obama’s critics may claim the Inquisition and the Crusades just weren’t all that bad (though an auto-da-fe in a capital case for, say, the refusal to eat pork, was probably about as “barbaric” as a beheading), I think Gilmore articulates the main objection: we’re in a “religious war” and the president needs to show solidarity with “our” religion. Others, of course, reject the idea of separation of church and state that Obama spoke of yesterday, typically by drawing on David Barton’s spurious histories of the Founders’ intentions.

But the deeper offense, I suspect, was caused by Obama’s return to the theme he articulated back in 2009 at a famous commencement address at Notre Dame: doubt as essential to faith, and humility as essential to obedience to God.

In my own commentary on the Notre Dame speech, I argued Obama was reviving an idea of the “fear of God” that fundamentalists had all but extinguished in their determination to claim divine sanction for their all-too-secular agenda of cultural conservatism and intolerance:

Fundamentalism, particularly in its political application, is typically based on the redefinition of “humility” as a rejection of civility and [of] mutual respect as an act of obedience to God, whose revelation of His will, through scripture, teaching or tradition, is so clear that only selfishness and rebellion could explain the persistence of doubt. This inversion of the “fear of God” as requiring aggressive and repressive self-righteousness has been responsible for endless scandals of faith over the centuries, quite often in conjunction with the divinization of culturally conservative causes from slavery to nationalism to patriarchy.

Obama was even more emphatic about that connection in his latest speech. And this sort of talk is why some conservative evangelicals and “traditionalist” Catholics deny mainline Protestants like Obama (and roughly 40 million other Americans) status as “real” Christians:

If we are properly humble, if we drop to our knees on occasion, we will acknowledge that we never fully know God’s purpose. We can never fully fathom His amazing grace. “We see through a glass, darkly” — grappling with the expanse of His awesome love. But even with our limits, we can heed that which is required: To do justice, and love kindness, and walk humbly with our God.

You can imagine how well this goes over with people who think God dictated the Bible as a sort of (to use the evocative analogy of former U.S. Rep. Paul, Broun, Jr.) “manufacturer’s handbook for how to run public policy and everything in society.” To them doubt is the opposite of faith; self-righteousness is an essential witness to the truth of faith; and tolerance or acknowledgement of the sins of one’s own community is unilateral disarmament in the spiritual warfare involved in converting the whole world.

This is one of many circumstances in which I hope the MSM, with their vast ignorance of religion, don’t take it for granted that the only “real” Christians are fundamentalist Christians, and the only true Gospel is one of belligerent nineteenth (or even eighteenth) century Americanism in politics, economics and ethics.

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Ed Kilgore is a political columnist for New York and managing editor at the Democratic Strategist website. He was a contributing writer at the Washington Monthly from January 2012 until November 2015, and was the principal contributor to the Political Animal blog.