Software filters are tuned more strictly for new accounts and kill some comments based on past behavior by spammers and/or trolls. We review the comments that have been killed that way (most of them, at least) and unkill the good ones and mark the accounts legit. But it takes us time to do that, which is one reason why user vouches are helpful.
To flag a comment your account needs a minimum score, I'm not sure, but I think it is 50 (or 100 or something).
To flag something you click on the timestamp on top of the comment (typically something like: <x> hours ago). This opens a view of only that comment and replies to it. If you have enough reputation/points/karma, you can now see a flag link on top of the comment. If you click flag it ends up in a moderation queue. If multiple users click flag it might bypass the moderation queue and become flagged immediately without further intervention from mods.
That's exactly what vouching is for: https://news.ycombinator.com/newsfaq.html#cvouch.
coryrc already pointed this out but I want to hammer the point :)
(Users have already vouched for the comment so it's no longer dead.)