To many, a comment that doesn't follow their personal logic or point of view is not a good comment. And you end up with echo chambers where only the comments that align with the majority of a community pop up, while the extremists (for lack of a better term) of a community are pushed to the bottom. Those extremists could easily be individuals sounding the alarm on something that's happening, such as skepticism for a story.
On Reddit and HN, I almost never downvote anyone because I think it's a terrible system that is too often abused and reduces the ability to have meaningful conversations about controversial topics.