Earlier quoted context omitted.
In this case, the algorithm is open, so there's no guesswork: http://www.righto.com/2009/06/how-does-newsyc-ranking-work.h... HN has normally been transparent whenever they modify something manually.
I've been noticing a pattern lately where anything that touches on a few different hot-button issues gets blasted away with flags the second it creeps onto the front page. I don't think its the mods having anything to do with it, but it feels a little broken.
It's a tough problem. Those stories often relate to important issues which hold intellectual interest, if not necessarily gratifying intellectual curiosity (the mandate of this site). In that sense they're not all off-topic. But it damages this site and community for it to host ideological flamewars, much as it damages a neighborhood to host rubbish fires.
My reading of the user flags is that they're partly trying to protect the neighborhood, and there's value in that.