But I recently submitted a link containing an uncomfortable truth from Pew Research titled "U.S. has world’s highest rate of children living in single-parent households".
It got 30 upvotes in one hour, and quickly reached the front page. It seemed to have gotten shadowbanned by a moderator, as it disappeared to the 5th page despite its quickly gained popularity. It was not flagged, or at least not normally as it would show "[flagged]". I suspect someone with special powers demoted it for whatever reason.
This was the post: https://news.ycombinator.com/item?id=26100329
It can be flagged without showing "[flagged]". That tag only gets shown when something is flagged to death. Your item wasn't flagged to death because it's still active.
I suspect it's mostly that a sizeable proportion of people on the site decided that it doesn't really fit with the theme and they don't want to see things like that, so they flagged it. That, associated with the large number of comments and comparatively few upvotes caused the "flame war" penalty to apply.
No conspiracies necessary, all explained by the regular dynamics.