Usually when the [flagged] marker appears, it's a combination of users who feel that the story is offtopic for HN (perhaps because it has already led to a lot of repetition and flamewars), and users who disagree with the article for ideological or political reasons.
If you think something valuable has been improperly flagged, you can mail hn@yc. What you shouldn't do is complain on the thread that it's been improperly flagged, because the meta argument you'll start by doing that will just make the story drop faster. Front page real estate is scarce, and the site is rigged to find every reason to push things off it to make way for the next valuable story.
More specifically, HN relies on a "flamewar detector", which signals overheated conversations where there are > 40 comments and the ratio of comments to upvotes is > 1.
Long digressions tend to push stories toward that threshold.
