Lears is only implicitly an apologist for religion. He does not attempt here a defense of faith or theology, except to take the by-now standard line that most believers aren't the literalist yahoos atheists assume them to be. Here's a sample:
[Harris's] critique of religion is a stew of sophomoric simplifications: he reduces all belief to a fundamentalist interpretation of sacred texts, projecting his literalism and simple-mindedness onto believers whose faith may foster an epistemology far more subtle than his positivist convictions. Belief in scriptural inerrancy is Harris’s only criterion for true religious faith. This eliminates a wide range of religious experience, from pain and guilt to the exaltation of communal worship, the ecstasy of mystical union with the cosmos and the ambivalent coexistence of faith and doubt.
On the specific question of Islam, Lears is at pains to absolve Islam of responsibility for Islamism, which he sees as the misguided expression of legitimate grievances against imperialism and oppressive governments. "Radical Islam often provides an idiom for their anger, but its centrality has been exaggerated," Lears insists. Likewise, he absolves Christianity of responsibility for the Christian Right, portraying the American movement as "the work of seasoned political players" designed to distract voters from "issues of justice and equality" and make the land safe for plutocrats. This sort of analysis shouldn't be dismissed automatically, but it should be applied universally. Lears wants to give Christianity and religion in general credit for progressive movements in American history, from the abolition of slavery to the resistance against the Vietnam war, but he can't give religion an amount of credit for good things equal to the amount of blame he refuses to assign to religion for the bad things. But it's been part of the left attack on atheism to argue that faith gives people hope, on the assumption that a more godless public will be a more hopeless public, and presumably more passive, selfish, etc. as well. This argument is often made by people who aren't especially religious themselves, and there's a note of condescension in it, an acknowledgment of the need for a "noble lie" to motivate the masses, as opposed to the enlightened elite.
What seems to irk Lears the most about Harris and the other atheists is their alleged "absolutist cast of mind," their oppressive "longing for clarity and certainty," and Harris's particular disdain for "relativism." Lears is an unrepentant postmodernist, affirming "the provisionality of scientific truth" and even, however carefully stated, the social construction of reality. Assertive certitude is not merely offensive to Lears; it's downright oppressive, not to mention, insofar as it rejects relativism, "perfectly consistent with the aims of the national security state." While the libertarian and many to his right cry, "Don't tell me what to do!" the postmodernist and many to his left cry "Don't tell that poor animist tribal person what to do!" Both sides share a visceral hostility to the idea that verifiable expertise might actually compel some degree of deference or emulation from others, or even that there are some questions so indisputably settled that further debate can only be counterproductive. They seek meaning from life either on exclusively individual terms or through a democratic consensus independent of if not hostile to objective considerations. The idea of objectivity itself is widely suspect in our age of bad faith. Lears's attack on Harris is an exemplary text of bad faith, ironically written in defense of "good" faith. I might agree with Lears on many "progressive" secular issues, foreign and domestic, but I'm left wondering whether Lears is really progressive at all.