The Boston Globe columnist Jeff Jacoby writes: "To hear his critics tell it, Pipes is an 'Islamophobe'", but in Jacoby's view, "these are gross and vicious libels."

Tashbih Sayyed, former editor of the Muslim World Today and the Pakistan Times (not the Pakistani newspaper of the same name), stated about Pipes, "He must be listened to. If there is no Daniel Pipes, there is no source for America to learn to recognize the evil which threatens it... Muslims in America that are like Samson; they have come into the temple to pull down the pillars, even if it means destroying themselves." Similarly, Ahmed Subhy Mansour, a former visiting fellow at Harvard Law School, writes, "We Muslims need a thinker like Dr. Pipes, who can criticize the terrorist culture within Islam."

In The Nation, Brooklyn writer Kristine McNeil described Pipes in 2003 as an "anti-Arab propagandist" who has built a career out of "distortions... twist[ing] words, quot[ing] people out of context and stretch[ing] the truth to suit his purpose".

Zachary Lockman, Professor of Middle Eastern and Islamic Studies and History, wrote in 2005 that Pipes "acquired a reputation in Muslim American circles as an 'Islamophobe' and 'Muslim basher' whose writings and public utterances aroused fear and suspicion toward Muslims". He stated that Pipes's remarks "could plausibly be understood as inciting suspicion and mistrust of Muslims, including Muslim Americans, and as derogatory of Islam".

James Zogby argues that Pipes possesses an "obsessive hatred of all things Muslim", and that "Pipes is to Muslims what David Duke is to African-Americans". Christopher Hitchens, a fellow supporter of the Iraq War and critic of political Islam, also criticized Pipes, arguing that Pipes pursued an intolerant agenda, and was one who "confuses scholarship with propaganda", and "pursues petty vendettas with scant regard for objectivity".

When Pipes was invited to speak at the University of Toronto in March 2005, a letter from professors and graduate students asserted that Pipes had a "long record of xenophobic, racist and sexist speech that goes back to 1990". but university officials said they would not interfere with Pipes's visit. Pipes wrote an article about his experience at York University, also in Toronto.

Professor John L. Esposito of Georgetown University has called Pipes "a bright, well-trained expert with considerable experience", but accuses Pipes of "selectivity and distortion" when asserting that "10 to 15 percent of the world's Muslims are militants". In summation, Esposito complains that equation of "mainstream and extremist[s] Islam under the rubric of militant Islam" while identifying "moderate Islam as secular or cultural" can mislead "uninformed or uncritical readers".

Ben Smith, in an article on Politico, criticized Pipes for what he said were false or misleading statements about Barack Obama's religion, stating that they amounted to a "template for a faux-legitimate assault on Obama's religion" and that Daniel Pipes' work "is pretty stunning in the twists of its logic".

Pipes was included in the SPLC Field Guide to Anti-Muslim Extremists that was removed from the SPLC website after Maajid Nawaz filed a lawsuit.