The author of the submitted blog post writes,
"One of the main reasons it doesn't work is that people don't ask questions to clarify. They jump to conclusions, some of which are very wrong."
I think that is the nub of the issue. People who are genuinely curious about an issue try to find out more. I routinely upvote comments here on any subject that ask for more information or more sources on factual statements made in articles submitted to HN or factual statements made in comments. We don't all have the same background in life experience and formal education, and I often learn new facts about the world from other Hacker News participants. I can't always assume that I understand another person's comment on the first read. Moreover, quite a few participants here write English as a second language. (How many Americans can write in ANY language besides English?) So sometimes the first thing to do when replying to an article submitted to HN is to ask follow-up questions. Another good thing to do is to point to other sources, if you know of any, for more information.
Civility is a core value of Paul Graham, the founder of Hacker News. He wants us to be able to disagree politely
http://paulgraham.com/disagree.html
when we do disagree, and the Hacker News welcome message
http://ycombinator.com/newswelcome.html
distills the basic rules of the site into a simple statement: "Essentially there are two rules here: don't post or upvote crap links, and don't be rude or dumb in comment threads."
Don't be rude. Don't be mean. That's not easy, but that is the community guideline here. Or maybe not being mean or rude IS easy, if you practice it. It's worth finding out how much we could all habituate improving our social skills by how we behave here on Hacker News.
AFTER EDIT: It's worth pointing out that I wrote all of the above part of what I wrote before I really wrapped my mind around the fact that, after all, the submitted blog post comes from Dave Winer, whose blog posts I have been reading for more than a decade. I still stand by my statement that we may all as well be as civil as we possibly can and as factual as we possibly can here on Hacker News. This is a community we can all improve by our individual actions. That said, I think Dave Winer and plenty of other bloggers have plenty to learn from the best comment threads on Hacker News, the comment threads that most follow pg's aspirations for this site, precisely because there is a back-and-forth in the comments and a fact-checking that many bloggers shy away from. The difference between a blogger and a journalist is that a journalist is a reporter who writes for an editor. Sometimes bloggers write only for themselves, and when they do, they can learn from comments, if only they are willing to do so. When a blogger writes about another public figure, the blogger has to be able to take the heat, or maybe the blogger should find another kitchen.