Most of the public controversy over the president’s remarks at this year’s National Prayer Breakfast involved his reminder that Muslims were not alone in harboring “sinful tendenc[ies] that can pervert and distort our faith.” By invoking the Crusades and the Inquisition as examples of violent and intolerant Christian iniquity, Obama provoked a few conservatives into actual defenses of these phenomena, including some that sought to reinforce the idea of an irrepressible conflict between Christianity and Islam. There’s little question the president was in part motivated by a desire to respond to almost constant conservative complaints about his unwillingness to identify terrorism with Islam.

But beyond the context of Christian-Islamic rivalry and comparative assessments of religious violence, Obama was also quietly but forcefully continuing an intra-Christian argument over clarity of God’s Will and whether those who assert they know it in detail are exhibiting faithful obedience or arrogant self-righteousness. There’s no question where the president stands on the question:

I believe that the starting point of faith is some doubt—not being so full of yourself and so confident that you are right and that God speaks only to us, and doesn’t speak to others, that God only cares about us and doesn’t care about others, that somehow we alone are in possession of the truth.

For Obama, as for many liberal Protestants, the “fear of God” connotes not only tolerance of other believers (and nonbelievers), but separation of church and state, which he treats as a practical application of the Golden Rule. And that, more than the specific challenge of how to speak about Islamic terrorists, enrages many conservative Christians, both “traditionalist” Catholics and evangelical Protestants. Consider this reaction from conservative blogger, radio talk host and Fox News “personality” Erick Erickson, who is also taking classes at a conservative Calvinist seminary:

Barack Obama is not, in any meaningful way, a Christian and I am not sure he needs to continue the charade. With no more elections for him, he might as well come out as the atheist/agnostic that he is. He took his first step in doing so yesterday in a speech reeking with contempt for faith in general and Christianity in particular….

Christ said, “I am the way, and the truth, and the life; no one comes to the Father but through Me.” (John 14:6) Christ himself is truth. When we possess Christ, we possess truth. The President is a moral relativist. It was clear in his whole speech…. To suggest that everyone can have some version of God and some version of truth is worldly babbling, not Christianity.

In this respect Obama is, consciously or unconsciously, standing in for liberal Americans—or to some extent, though the overlap is not total, “mainline” Protestants or “modern” Catholics—who do not subscribe to biblical inerrancy, spiritual exclusivity, or the sense that Christians are a besieged or even persecuted community marked by conservative cultural commitments that separate them from a wicked world. Such Christians are quite a large group, even though they are often ignored by secular observers who buy the idea that the only “authentic” Christians (or “Christian music,” or “Christian films”) are conservative. More than 26 million belong to the “mainline” Protestant denominations, and more than 60 percent of American Catholics favor some or a great deal of adjustment to tradition in accordance with “modern needs” (57 percent oppose church teachings on same-sex marriage, to cite one example of the “moral relativism” that involves). And after decades of hearing that liberal Christianity is dying, there’s actually fresh evidence that among millennials the much-discussed trend towards unbelief disguises an even sharper trend towards “moderate” positions among the majority that are believers.

But if Obama does represent a still-vibrant American Christian tradition, he’s lost support among many potential allies by constant and fruitless gestures of solidarity with the very conservative Christians who deny the legitimacy of his faith. Indeed, his dogged determination to appear at the conservative evangelical-sponsored National Prayer Breakfast, where (as Sarah Posner of Religion Dispatches points out) he and people like him are regularly vilified, has become a religious analogue to the paens to bipartisanship that have so annoyed progressives since he took office. An entire Republican presidential candidacy—that of “base” favorite Dr. Ben Carson—emerged from his “courageous” criticisms of the president (in his presence, of course) at the 2013 event. And even at this year’s breakfast, the message of the “non-controversial” keynote speaker, NASCAR driver Darrell Waltrip, was a very blunt contradiction of the president’s injunction to humility about religious truth:

If you don’t know Jesus as your Lord and Savior, if you don’t have a relationship [with Him], if He’s not the master of your life, if you’ve never gotten on your knees and asked Him to forgive you of your sins, [and] you’re just a pretty good guy or a pretty good gal, you’re going to go to Hell.

Not much holy doubt in that mind, is there?

Oddly enough, the general tenor of the commentary on Obama’s remarks at the breakfast is that he was being defiant or “provocative;” one conservative even accused him of “verbal rape.” Seems to me he was turning the other cheek.

Ed Kilgore is the principal blogger for Washington Monthly’s Political Animal blog, Managing Editor of The Democratic Strategist, and a Senior Fellow at theProgressive Policy Institute. Earlier he worked for three governors and a U.S. Senator. He can be followed on Twitter at @ed_kilgore.