If you'll be penalized for saying something people disagree with, you won't say it, or you'll say it and I'll be downvoted until it's hidden. This leads to HN threads usually being dominated with a few majority opinions and any real discussion being killed-off or buried.
This is basically the same as Reddit. If you want real discussion you often need to sort by controversial.
At least for now I find them useful. I have read a lot of grayed posts to get a feeling for what's going on and usually see why. I've upvoted a few where I thought the author was on point.
I believe you get access to downvotes after 500 karma, and only for up to a day after the comment was made