Compared to some other major world religions, Harris considers Islam to be
"especially belligerent and inimical to the norms of civil discourse." He asserts that the
"dogmatic commitment to using violence to defend one’s faith, both from within and without" to varying degrees, is a central part of the doctrine of Islam not found in many other religions,
"and this difference has consequences in the real world."
In 2006, after the Jyllands-Posten Muhammad cartoons controversy, Harris wrote, "
The idea that Islam is a 'peaceful religion hijacked by extremists' is a dangerous fantasy—and it is now a particularly dangerous fantasy for Muslims to indulge. It is not at all clear how we should proceed in our dialogue with the Muslim world, but deluding ourselves with euphemisms is not the answer. It now appears to be a truism in foreign policy circles that real reform in the Muslim world cannot be imposed from the outside. But it is important to recognize why this is so—it is so because the Muslim world is utterly deranged by its religious tribalism. In confronting the religious literalism and ignorance of the Muslim world, we must appreciate how terrifyingly isolated Muslims have become in intellectual terms."[6][9][38][39] He has voiced support for profiling, stating,
"We should profile Muslims, or anyone who looks like he or she could conceivably be Muslim, and we should be honest about it."[40] He states that his criticism is aimed not at Muslims as people, but at the doctrine of Islam as an ideology, acknowledging that not all Muslims subscribe to the ideas he is criticizing.
Anthropologist Scott Atran has criticized Harris for what he believes is
an unscientific highlighting of the role of belief in the psychology of suicide bombers. Atran later followed up his comments in an online discussion for Edge, in which he criticized Harris and others for combating religious dogmatism and faith in a way that Atran believes is
"scientifically baseless, psychologically uninformed, politically naïve, and counterproductive for goals we share".[41]
In an article in The Nation reviewing three of Harris’ books, Jackson Lears, states that, when Harris’ arguments are evaluated "according to their resonance with public policy debates, the results are sobering...", continuing:
"From him we learn, among other things, that torture is just another form of collateral damage in the "war on terror"—regrettable, maybe, but a necessary price to pay in the crucial effort to save Western civilization from the threat of radical Islam… As in the golden age of positivism, a notion of sovereign science is enlisted in the service of empire. Harris dispenses with the Christian rhetoric of his imperialist predecessors but not with their rationalizations for state-sponsored violence".[42]
Several columns, one in Al Jazeera and one in Salon, have accused Harris and the New Atheists of expressing irrational anti-Muslim animus under the guise of rational atheism, Glenn Greenwald wrote a column saying he agreed:
"The key point is that Harris does far, far more than voice criticisms of Islam as part of a general critique of religion. He has repeatedly made clear that he thinks Islam is uniquely threatening … Yes, he criticizes Christianity, but he reserves the most intense attacks and superlative condemnations for Islam, as well as unique policy proscriptions of aggression, violence and rights abridgments aimed only at Muslims.".[40] Harris has responded to the controversy stating that he believes critics of Islam are unfairly labelled as bigots.[43][44]
Harris has criticized the term "Islamophobia". "My criticism of Islam is a criticism of beliefs and their consequences," he wrote following a controversial clash with Ben Affleck in October 2014 on the show Real Time with Bill Maher, "but my fellow liberals reflexively view it as an expression of intolerance toward people."
"Islamophobia is a term of propaganda designed to protect Islam from the forces of secularism by conflating all criticism of it with racism and xenophobia. And it is doing its job, because people like you have been taken in by it."[6][45]