He's also advocated profiling anyone who looks Muslim.

We should profile Muslims, or anyone who looks like he or she could conceivably be Muslim, and we should be honest about it. And, again, I wouldn’t put someone who looks like me entirely outside the bull’s-eye (after all, what would Adam Gadahn look like if he cleaned himself up?) But there are people who do not stand a chance of being jihadists, and TSA screeners can know this at a glance.

http://www.samharris.org/blog/item_working/in-defense-of-profiling

Needless to say, a devout Muslim should be free to show up at the airport dressed like Osama bin Laden, and his wives should be free to wear burqas. But if their goal is simply to travel safely and efficiently, wouldn’t they, too, want a system that notices people like themselves? At a minimum, wouldn’t they want a system that anti-profiles—applying the minimum of attention to people who obviously pose no threat? We should profile Muslims, or anyone who looks like he or she could conceivably be Muslim, and we should be honest about it. And, again, I wouldn’t put someone who looks like me entirely outside the bull’s-eye (after all, what would Adam Gadahn look like if he cleaned himself up?) But there are people who do not stand a chance of being jihadists, and TSA screeners can know this at a glance.

I remember thinking those ideas were pretty stupid when I first read them, because all of the 9/11 attackers were clean-shaven, wore western clothing, and even drank alcohol, taking great pains to blend in. Seems like his suggestions would have the TSA focusing on obvious Muslims, who aren't trying to hide, compared to the more subtle, dangerous individuals trying to blend in.

And see this recent piece regarding ISIS http://aranews.net/2016/01/17574/

The Islamic State provides in its new release suggestions for Western terrorists, including shaving beards, forgoing religious clothing and wearing crucifix necklaces.

“It is permissible in such cases for you to wear a necklace showing a Christian cross,” the radical group advises its followers in the West. “As you know, Christians (or even atheist Westerners with Christian background) wear crosses on their necklaces. But don’t wear a cross necklace if you have a Muslim name on your passport, as that may look strange.”

I also thought he kinda seemed like a neo-con, particularly the stuff he said about the Iraq war being a civilizing mission. But calling him a bigot the way Greenwald does is pretty fucking stupid and does nothing to meaningfully rebute his ideas.