According to Spencer Ackerman at Wired, the FBI has taught counterterrorism agents that mainstream Muslims are "likely to be terrorist sympathizers," that devout Muslims are likely to be violent, and that their tradition of giving to charity has been turned into a "funding mechanism for combat." In response, the FBI said the leaked materials Ackerman cites in his report were part of a "one time only" training seminar that was "quickly discontinued" six months ago. Is this evidence of anti-Muslim bias inside the FBI?

Yes. The FBI is obviously biased: The lesson in this training session was "clearly Islamophobic," says Eli Clifton at ThinkProgress. Of course, it's not true that devout U.S. Muslims are more likely to support terrorism — "in fact, mosques have been found to be a deterrent to the spread of terrorism." And don't believe that this was a one-time deal. The FBI has exposed agents to lectures by several Muslim-demonizing "pseudo-experts."
"New documents reveal FBI's Islamophobic counterterrorism training"

The FBI training wasn't without merit: This isn't anti-Muslim bias — it's the truth, says Robert Spencer at Jihad Watch. Sure, mainstream Muslim groups condemn al Qaeda and 9/11. But many also have ties "to the jihad terrorist group Hamas and its parent organization, the Muslim Brotherhood, which is dedicated to imposing Islamic law around the world." The FBI didn't do anything wrong — its trainers merely depicted Islam accurately.
"Far-Left 'journalist' assails FBI training materials that depict Islam accurately; FBI folds"

And Islam isn't the enemy; terrorists are: After 9/11, George W. Bush made it clear "the United States was not at war with the Islamic faith, but with terrorists who were using their religious faith to justify a murderous agenda," says Doug Mataconis at Outside the Beltway. Only wingnuts want a "Holy War against Islam." Letting their nutty ideology seep into the FBI isn't just wrong — it also "reduces the ability of agents to detect actual terrorism."
"FBI using anti-Muslim literature to train counterterrorism agents"