If that were the only way it was used it would be fine. But it is also used to simply shut down rational discussion on subjects the flaggers don't like.
So in that respect, I often agree with the submissions that get flagged (including this one), but I do think news.ycombinator.com could do a better job of collecting and displaying these flagged submissions. For example, duplicate submissions could be made children of the submission that was allowed to stay.
The biggest gripe I have with the flagging is the paternalistic aspect.