That seems to be more the result of the overzealous flame-war detector rather than the effect of flagging. Only PG can truly tell, though.
The flamewar detector brings the story down if it has a lot of comments, and if not paired with lot of upvotes, takes it quickly off the front page. So, while you're right about the HN bias(lack of upvotes), you're wrong about the reason(flamewar detector rather than flagging).
It also tends to happen to Gruber articles, articles positive or neutral about Microsoft, and anti-Samsung or anti-Google articles.
Here's a couple of examples.