Stories about colonialism sometimes get flagged, presumably because they give rise to ideological and (worse) racial and national flamewar. But there have been many on Hacker News' front page over the years, as well.

The thing to watch out for with such perceptions, besides sample bias, is that we're all more likely to notice what we dislike than what we agree with. If a story I like gets flagged, that registers far more strongly than a story I like not getting flagged. So even a perfectly even-handed forum will seem unfair and biased in any area you feel strongly about. Not that HN is a perfectly even-handed forum—but what's going on is a lot more stochastic than these perceptions seem.

Edit: having looked at the story, I think probably what tipped the balance for flags over upvotes was the obviously baity title. Threads are sensitive to initial conditions, and a title like that guarantees a bad thread, regardless of how justified it might be. I've edited the title and turned off the flags.