Homeland surprised everyone when it started by changing the face of terrorism, literally: the primary suspect was Sergeant Nicholas Brody (Damien Lewis), a white American man who had been "turned" while he was a POW. It was an interesting departure from the usual "othering" — the show's creators didn't only use a Muslim character to embody the face of evil and villainy.
But in the show's three seasons, not much has changed in the way of further separating the face of "terror" from Islam. Yes, Abu Nazir was the central threat for much of the show's first two seasons; but now, in its third, Homeland still stands on those same legs. At Salon, Daniel D'Addario makes note that Homeland uses crude visual cues to signify that every Muslim on the show is a threat:
In the current season, a CIA analyst played by the Iranian actress Nazanin Boniadi has changed the temperature on Homeland without doing much of anything. Boniadi’s character, Fara Sherazi, is explicitly a potential threat; in a show whose very nature lends itself to constant betrayal, the camera lingers over her rather anodyne presence as though her hijab signals treason in the offing.
It's relying on the same tropes that it began with, and doing nothing to distance itself from Islamaphobia. D'Addario also keenly points out that it is beginning to make the show feel dated, like the paranoia of the immediate climate post-9/11.
There are other avenues for Homeland to explore, though; in recent years, many terrorist attacks have been carried out by non-Muslims, forcing America to reformulate its image of the face of terror. After white men were found guilty in Tucson, Newtown and Aurora, there then started a conversation about WHO the enemy was — white terrorists were a reality.
Homeland does not seem to want to broach this subject yet; but it has to change its fixation on Muslim suspects, and soon, lest they pigeon-hole themselves as a show that feeds a desire to "other" members of Islam.