I agree entirely with the author's cause and I believe that the guilty-until-proven-innocent mindset of present airport security is wrong and should be unconstitutional.
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.