The same bait (sensationalism, indignation) that makes many users upvote those posts is what makes other users flag them. This rise and fall has always been the pattern on HN—it's one of the cycles of life here.
Right now, it's super sensitive where a little signal does a lot right at the beginning.
Stories rocket to the top because they're new and got a number of quick votes. The curve needs to be smoothed out so that things don't lurch to the top.
Edit: I've been around here for a little while. It used to be awesome to see things jump to the top (used to have a lot lower volume of posts and users), but the audience has changed a lot, and I think things need to be adjusted a bit to slow the meteoric rise aspect. Good content will surface.