I think the real issue of requiring comments on downvotes is that it would either disallow anonymous downvotes, or encourage anonymous comments. Perhaps de-anonymizing downvotes without requiring a comment might be a better first step: if you aren't brave enough to have your name associated with the downvote, then maybe you shouldn't be downvoting. I'm sure this would cause its own problems, but I suspect it would be a net positive. At times I think it might even be good to have all voting and flagging actions on HN to be public record.
On HN, unpopular comments are, often, still voted down despite the facts and despite the presentation.
I usually reserve these instances for when I know more than a little on the topic, generally professionally speaking, and often first hand. But, if it is unpopular, it doesn't matter. It's predictable.