People will flag articles when they don't feel safe to participate in the discussion, especially if they hold views that appears to be dissenting. An open and thriving environment for discussion is one that welcomes people of different views and opinions.

A strong indicator of an article that get flagged, and which also trigger the flame war detection on the site, is a bunch of comments that are either grayed out or flagged. The one will feed the other into a death spiral for the article.