I'm sure those complaining have valid points, my only counter to this would be..at the risk of over simplification...when was the last time a Hindu, Buddhist, Atheist, or Christian hijacked an airliner with a view to martyr themselves and their unwilling cargo as a legitimate act against a state or ideology?
I'm not saying the searches are justified or even right, they are however very easy to understand in the present climate of fear and prejudice.