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Reading that, I can say two things, based on my own (admittedly limited) knowledge and experience:
1) The writer of that article was, indeed, right. To my understanding, the officers WERE wrong in what they were doing. Customs officers at ports of entry can look through bags (import/export/smuggling/etc.), check passports, and inquire citizenship. However, if the person presenting himself is a US Citizen, all he has to answer are the most basic of questions (such as citizenship).
2) The writer of that article precipitated the confrontation deliberately with his manner. A simple "I'm sorry, but I'd rather not say," or "I prefer not to answer that question," delivered with a smile, goes a long way. It lets the officer know that A) you know your rights, and B) you're not trying to enter a "contest" with them. It draws a line, yes, but it doesn't dare the officer to cross it. Being confrontational/rude is akin to telling them "so what ya gonna do about it, punk?" and can lead to poorly considered actions all around. Remember, just because you CAN be rude and within your rights does not change the fact that you're still being rude and confrontational.

It is far better to be cognizant of your own rights, while still respectful of those hired to enforce the laws. Getting into a match of wills with individual agents of the law is not the way to beat laws you disagree with, or overcome overreaches of the law. All it does is let everyone around know that you've got a chip on your shoulder and are trying to prove something in petty fashion. Far better to extend the olive branch of politeness and respect, while refusing to give in to overreaches.