This is one of the major problems with unregulated and unsupervised NSA activities (and other agencies). We've seen them blatantly lie about their actions, to the public and to congress. They've lied under oath without any repercussions.
I don't know if I can believe any official reports. They say the FBI wasn't involved, and I believe them but "they" have proved unreliable in the past. This is the fertile soil for conspiracy theories and it's the governments own fault.
We're left with Occam's razor. Mr. Mukerjee was probably feeling a little hot-headed that day and maybe he mouthed off to the first TSA guard who placed him on some list. He probably doesn't like or trust the TSA since he opted out of their preferred method of scanning. It's pretty believable that the agents don't know much about hinduism since they are not targeting potential hindu terrorist, but extremist muslim terrorist (if you consider terrorists true muslims which I don't). It seems likely that he set off multiple security alarms. Police TSA aren't going to know about venture capital or care about your job. They are just asking to see if you slip up or act nervous. Israeli security simply asks "how are you doing today" not b/c they care but b/c a persons reaction tells them a lot and they will drill down if you get agitated by their questions.
In the end, Mr. Mukerjee did nothing wrong. He got agitated by something that would anger all but the most patient individuals. That's actually the scary part. Al-Qaeda and other terror groups have shown again and again that they are VERY patient and persistent. One of their agents would probably have gone through the main scanner and if detected remain very affable and friendly with the TSA.