Downvotes on reddit are used for posts that are nonconstructive / completely offtopic, as a means of filtering them.
It’s stronger than not upvoting, and I think it’s the main reason of Reddit’s popularity and it’s major strength…it crowdsources moderation.
An explanation can be added as a reply, but it’s usually not needed at that level, and in many cases is a waste of energy.
It’s also used to measure the quality of the comments and then order the threads better, which is huge when there are a lot of comments, but the main advantage for me is hiding the negative ones when I don’t have time to read everything.
Something can be said about downvotes based on opinion for lack of understanding, to solve that a popup should ask for confirmation by default (Are you sure this comment is off-topic or not constructive?)
If I want to filter all comments bellow a certain level (say 0) and there is no downvoting, then I will filter comments that did simply not get any votes because they were not exceptionally good or bad.
You could add a button to report spam, then hide the comment after a number of spam reports, but that does not take into account the ratio of upvotes / downvotes so it’s not as good.