I applied for my Visa in Riyadh, Saudi Arabia. Only one Arabic gentleman at the embassy had problems when I was there - and that was due problems regarding his trip to Cuba.
It seems you got a short straw.
And yes, I agree with you - they do treat you like terrorist - until proven otherwise, rather than the other way round.
This has hit the tourist and Flying community alike over in the US.
Sorry to hear of your troubles - keep your chin up and good luck with your flying.