That's true. Then again, however, if a story is important enough to the community, it will get reposted—sometimes many times, either with the same URL or a different one. It's not so easy as people assume for flags to suppress that kind of story.

The submission you linked to (https://news.ycombinator.com/item?id=46357887), however, was not that kind of story (i.e. one which the majority of users want to see on the frontpage). Rather, it was the kind of story that some users want to see on the front page, but not the majority of users*.

It's the latter class of story which is more vulnerable to flags. That's generally what we want in a flagging system, and I think most HN users would agree with that in principle (though not of course in specific cases where the story is something that one personally finds interesting).

* This is predictable from its skeleton, btw: "person X says provocative thing Y about divisive topic Z" is usually not significant new information (https://hn.algolia.com/?dateRange=all&page=0&prefix=false&so...)