Of course users flagged it. Boring though it may be, that's usually the explanation. The [flagged] annotation shows up when the flags cross a high threshold. Posts without URLs also get a standard penalty.
Cherry-picking a single detail from a complex body of information does not make for a good HN post, because it's too editorialized: the one who cherry-picks that detail essentially determines the story for everyone else. When the subject is political, multiply this paragraph by 10x; when it's inflammatory, by another 10x.
This and other comments of yours use phrases like "silently hidden" which suggest manipulation of the site for political ends, but we don't do that, and everything that happened to this post and its follow-ups (12840284, 12844254) was completely standard. They're just not good posts for HN, and as they get more meta (e.g. "why was my post about why was my post flagged flagged"?), they get worse and worse.
