It's good to flag the ones that aren't a good fit, but please leave intact the ones on obscure topics. More explanation at my sibling comment (https://news.ycombinator.com/item?id=22990237).
Also, what happened to the "vouch" button?
What are some cases where you felt like this was happening?
It's true that flagging doesn't work perfectly, but it works better than many major features of HN. For example, it works far better than the upvoting system. Upvotes alone would kill the site [1].
There's a tug of war between upvotes and flags [2]. Some users flag because they personally dislike or disagree with an article, but when an article gets many votes, those flags aren't enough to win the tug of war. For flags to win, there needs to be a coalition between that group and a (usually larger) group of users who feel that the submission breaks the site guidelines somehow, or that the topic has been repeated too much and the new article doesn't contain significant new information [3].
HN's system consists of community, software, and moderation. When one part of the system fails, another part exists to address the failure. For example, when moderators fail, the community lets us know. When the flagging system fails, in the sense that an article that is on-topic and interesting gets unfairly flagged, it's the moderators' job to correct that when we review the flagged items. Community members can speed that process up by emailing hn@ycombinator.com.
[1] https://hn.algolia.com/?dateRange=all&page=0&prefix=false&qu...
[2] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
[3] https://hn.algolia.com/?dateRange=all&page=0&prefix=false&qu...
It only appears on things that are flag-killed, not just [flagged]