I can't say I understand the example supplied. There's no way to say what the commenter said to someone's face without being insulting; he is explicitly implying that Joel is being manipulative and deceitful. It's the sort of thing you can feel free to think to yourself, but which is very rude to say.

Try this: Say this paragraph out loud, and find a tone where the primary message conveyed isn't "way to pull one over on us, asshole" (hint: there isn't one.)

You disguise a PR piece as an objective 'how to' in a national business publication, coming across as an authority, the underdog, and an all around nice guy who really cares about his customers. You're an engineer who claims to be 'weak' in the sales department, but all evidence to the contrary: nice 'sales hack'.

Even if you got rid of loaded words like "disguise" and took away the scare quotes, there's still no nice way to express that thought to someone. It's really tactless; any reasonable person would be insulted, regardless of the medium.

To generalize, I posit that a lot of "miscommunication" thanks to tone online is just a result of people feeling free (with the cover of semi-anonymity) to throw away any subtlety and confront people in a manner that they would never adopt face-to-face.

EDIT: Expanding on my last paragraph, I don't want to be overly critical of people who are very straightforward and speak their mind online, even if it seems rude; there's certainly a tradition of abrasively practical hackers. The commenter perhaps did everyone a service by opening for discussion something that other people might have left unsaid.