After reading this article, I'm halfway tempted to think that his incident was an elaborately orchestrated plot to facilitate a power grab by the FAA:
Excursus: When the FAA was in danger of "losing 4,000 jobs", I thought to myself, "what the hell does the FAA need with 4,000 employees" - can't we deploy Skynet already?
What stops the Feds from simply claiming anyone they want to investigate is a "suspected terrorist" and doing all the snooping they want. Suppose the Feds simply declare that due to "secret" information, they believe that someone is a "suspected terrorist". They tap his phone, bug his car, break into his email accounts...and discover that John Doe buys personal use quantities of prescription pain meds without a prescription. (but is not a terrorist). Or some other low-end crime.
Can the Feds put John Doe into prison based on this information?
I was just about to post to this effect - you're spot on.