Homeland Security is the product of paranoia and fear. Not ever Muslim is a terrorist suspect. The average Muslim here or in the Middle East is most likely far more concerned with everyday matters rather than acts of violence. Thanks to the security measures implemented we now racially profile everyone of Middle Eastern ethnicity.
Homeland takes a nuanced, complex look at the issues surrounding global terrorism, from it's initial financing up until the logistic of the actual attacks. Those who flatly dismiss Islam simply as a violent, hollow religion and espouse the blunt, knee-jerk Islamaphobia championed by the extreme right will not find their cause coddled in 'Homeland'. As much as the show centers around Islam, and it's role in global terrorism, the real motivator shown to be flipping and controlling possible terrorists has been demonstrated time and again to be intense psychological manipulation and the leveraging of fear and anger. Islam, much like other religions, is simply used as an excuse, a middle-man employed to propagate terrorists. Essentially, 'Homeland' is too smart and complex to stoke the flames of Islamaphobia, and people dull enough to buy into the idea of a religion composed of a billion terrorists lack the ability to comprehend the plot twists and will revert back to their '24' DVDs, instead.
Some of the loudest flag wavers behind the concept are, but Homeland itself isn't Islamophobic. Look at people like Santorum and Bachmann if you want to see what Islamophobic looks like. There's without question a culture that exists in this country that is absolutely mortified by Islam but I don't think it's fair to draw a direct line between it and Homeland Security.
I don't think that the show "Homeland" is Islamaphobic because I believe it's just portraying what is actually going on around us at the moment especially the war. It's a show that is not made to put down a particular nationality, it instead, enlightens our insights on what we all need to do in order for us to be a strong nation and work on improvements of securing our "Homeland".