I often see a question posed by a novice, whose rep. is 1. The question isn't good, so gets downvoted. Can't understand what the point of that is - their rep. can't go lower, what am I missing? A comment is so much more useful, or is that just too much effort?
You should check this meta post.
Downvoting a bad question helps with automatic clean-up of the SE sites. So even if you think it is useless to downvote a really bad question from a a new user with no score yet (actually a score of 1 if you want to get technical), it helps in keeping the site free from questions that does not bring anything useful to the site.
The SE system is programmed to auto-delete questions (and answers in some cases) without any action from any type of user, mod or network admin. This is done to clean up any non-useful questions or questions and answers which has been flagged as spam and abusive.
If we look at points 8 and 9 in the linked meta post we will see the following
The system will automatically delete unlocked, unanswered questions that have negative score after 30 days.
The system will automatically delete unlocked, unanswered questions with score of zero (or one if the owner is deleted), fewer than 1.5 views per day on average, and fewer than two comments after 365 days.
If you take these into consideration, downvoting a bad question will have it removed in 30 days from the site, whereas it will normally take a full year to do so if question remains with a score of zero (this is, if these questions does not recieve any answers).
So, questions does get auto-deleted by the system based on just the total score of the question without any user casting a close votes or being closed by the community or mod, provided that that specific question has not received any answers.
Apart from this, as @Dom stated in a comment, 10K+ users can only cast delete votes on a question when that specific question has a negative score.
I think we all should stop thinking that downvoting is there to punish a user, because it is not. It is a tool, if used properly, to keep the site clean from poor content or content that doen not fall in scope of the site. Some system or user cleanup actions can't happen if a question (or answer) is not downvoted.
As last thought, a downvote sometimes forces the poster to self-delete his own post or correct the post to bring it up to standard, and remember, downvotes can be removed if the post was edited in such a way to bring it up to scratch
The SE system also have an automatic answer/question ban system, if a user keeps on posting bad quality posts, and get enough downvoted, the system will apply a answer or question ban on the user, which again prohibit a user from posting anymore useless crap. This ban is almost permanent as it is almost impossible to get this removed. This ban can only be removed by the system itself.
Question quality block enabled on all SE sites, so this will really make your vote (or edit) count on questions.
The downvote privilege is at 125 reputation; Close (and reopen) is at 3000 reputation. There are users whose only means of negative feedback is to down vote.
Whether or not it affects the user's reputation, marking a question with down votes indicates that the voter thinks that it is not a "good" question in one way or another. This may be an indication to the OP not to post such questions again, or as a warning to other people who come across the down-voted question in the future.
Also, I believe that there is a mechanism where if content receives enough down-votes it gets put into a queue for further review; thus is it sort of a weak form of flagging.
See the top answer on this post on meta.
The comments are there for people who want to explain their downvotes.
The only thing I can think of is an AJAX reminder for users when they cast downvotes:
Please consider adding a comment if you think this post can be improved. After the first downvote, we can't say we didn't remind them, and honestly that's as good as it gets. Forcing a comment will end in even worse results.
edit: this is now status-completed and live for users with reputation below 2000. It is shown on every downvote until you get to 2k.