I understand (and I'm not suggesting something has changed with the system recently) but personally I have seen a lot of big stories get flagged within minutes of reaching the front page despite have large, useful discussions within the comments. Normally these stories have a political bent or are world news stories that involve guns, terrorism, immigration and other similar topics. I have seen how comment sections on those topics can descend into useless arguments but often there is still useful content and relevance to technology.
Does the number of comments on a post get taken into account along with votes and flags? It seems to me that if a story is polarising people who disagree with it will be much more liberal with their down vote whereas people who may agree with it are taking the time to read and comment instead of immediately voting.