I got more questioning from US immigration than my Indian girlfriend, mainly as I had a Moroccan stamp in the passport - they were very chatty and friendly and it took a couple of minutes. I assume you mean they looked at your passports first?
Possibly you were the n th person through and got a search?
Would suspect that the stamps in the passport have more to do with it than ethnic origin, since although those men on 9/11 were Western in dress and apparent attitudes, the passport stamps would show their more suspicious travels I would imagine.
Also being Indian, surely you are Caucasian?! Just Indian caucasian rather than white caucasion...