Not only does the TSA pull aside more Muslims than any other group for special attention, but passengers often distrust and report people who are Muslim or who appear to be Muslim. It may not be the airline's policy to discriminate, but they take passengers reports seriously, often to the harm of innocents.
Muslims suffer discrimination in many areas, from the banning of headscarves in France to the degrading treatment they receive in America when they simply try to take a flight. They are routinely asked in for "further examination" in security lines. More seriously, there have been moves made towards outright banning Muslims from flying at all.
I don't think Muslims should be "discriminated" against, but after past events I think it is justified if they are subjected to increased security measures. It is unfortunate that we have to take advanced measures but I thunk in the end it is erring on the safe side. Muslims should still be treated with respect and courtesy, though.
Let's be honest, even if you are not a prejudiced person you are still going to look sideways if you see a Muslim gentleman in full garb walking onto a plane that you are riding in. After September 11th we are all a little hyper-sensitive toward this image. Even if you don't mean to discriminate you are going to consciously or unconsciously treat them differently.