That's just to help get them back to neutral, and avoid their point being grayed out and thus probably more likely skipped over by others. I think everyone should be allowed to put across their point, and we all end up better for seeing those different angles.
I quietly hope that others who agree with this also do the same, thus making the problem you describe a little less pronounced. We all need to play our role in creating the kinds of online communities we want to see.
I think people are more likely to think about voting when they see a downvoted post.
PS: I also feel some net negative posts are a good sign that someone is not simply voicing the crowd's opinions.
So it is a thing that happens, at least to a certain extent.
Has this reputation changed much?
If I've got tools to block sources of clickbait, and those feed into reputation systems, that's a start. On Google's properties, I can block G+ posters, but I cannot block a YouTube channel. Not even if I'm logged in -- that channel will still show up in searches and recommendations. I'm actually better of not logging in so that recommendations are keyed far more to current search and view history, and there is no long lag of "you watched this once three years ago so we'll cram it down your throat".
For Web, I've taken to fairly ruthlessly blocking clickbait domains at the firewall. They pretty much completely disappear.
(And, if I've got second thoughts or want to poke through: archive or simplified-view sites will generally show me the content. And it's almost never worth looking at.)
I'm not saying that my individual tools will scale out, but if they're tied in to larger systems, and feed back to what's promoted, there's the possiblity of this.
Ultimately, though, massive media channels have to take an active voice in what they do or don't permit, most especially where there are real and serious harms possible. That's the editorial voice option. It's not a popular opinion on much of the Web, and it's not one I would have advocated even just a few years ago, but I'm coming to feel it's increasingly proving necessary, and that the historical record, over the past 500 years of mass communications, starting with the printing press, bears this out repeatedly.
Free speech is not a responsiblity-free zone.
I.e., the stuff that is upvoted by people who "upvote like you" is ranked higher. (I would like this feature on HN, as it would eliminate e.g. articles about CSS which I find boring; of course that is personal, but that's the point).
Otoh, there's a danger of "echo chambers"; not sure how to deal with that.
If you want an example of the opposite approach, you can always look at 2009-era YouTube, when all comments shown were in a strict "newest" order. If you remember, YouTube had a bit of reputation for some of the lowest-quality comment sections anywhere.
There simply is no "quick fix" for clickbait, aside from altering basic human psychology, or some type of (probably complex) regulation.