I don't think it is immoral discrimination for an airport security officer to be a little more scrutinizing of a muslim or arab than a five-year old blue-eyed Texan girl.
It's not only immoral, it's stupid.
Crashfrog touched on this, but let's get more specific for a moment... let's assume for the moment that al-Qaeda puts two operatives in line at an airport. One of them is the perfect Middle Eastern stereotype. He's got a long, scruffy beard, a turban, and every third word out of his mouth is "Allah". The other is John Walker Lindh.
Lindh has been shaved, gotten a neat haircut, and is wearing a fancy three-piece suit.
To pay more scrutiny to the arab in this situation would simply provide al-Qaeda with an excellent deflection technique. Distract your attention with the arab, and let Lindh walk on through unmolested, with enough explosives to take out a plane full of innocent people.