That's like saying, you are just making trouble when you resist a pick-pocket or robber. You are never "just making trouble" when you assert your rights. On the contrary, government is the one just making trouble.
The only legitimate purpose of government is to protect rights. However, government seems to be full of people who are eager to take away rights. Somehow, the institution of government appeals to people who like to force their will on others. If you value liberty, you must resist these people.
One of the things the US is supposed to be really big on is freedom from Big Brother. Having legally entered his own country, not attempting to get on another plane, and offerring to cooperate as long as someone, under color of authority, would verbally go on record that he was required by law to do so, with specifics. Nobody was willing or able to actually do this. Nobody was clear about jurisdiction. The police wouldn't do anything without the TSAs instructions.
The TSA didn't know what's up - and I for one would like the people in charge of security in the airport to know what's up, right?
EDIT: From the sounds of things this really was more about poor airport design and people flow as well as misunderstanding of policies.
Like it or not, this kind of behaviour either strengthens the laws or removes poorly designed ones. Either way, it's important that people do this on a regular basis because laws and procedures are very rarely correct.
However, upon reading the article I very much got the impression that the author was refusing to be scanned or searched just to make trouble. When asked why he was refusing to be searched, his answers (in his own writing) seemed to be along the lines of, "because I don't feel like it." I'm sorry, but that's just not really a valid defense. Whether you feel it's constitutional or not, the law says you have to go through these checkpoints when selected. If you're going to refuse, you need to have a much better reason than you don't feel like it.
Ultimately, it sounded to me like they escorted him out of the terminal simply because they were tired of dealing with him, not because he found a loophole in their logic or rules. Less well-mannered officials would have put him in jail for a judge to deal with in the morning.