This question already has an answer here:
Upvotes and downvotes are different on Meta, a lesson lots of users learn every day on SE. Often one's first experience with this results in "Why downvotes" or "Could someone explain why this is getting downvotes?"
Thinking out loud, but how about some sort of just in time message saying something to the effect of:
Stop right there criminal scumDownvotes on Meta are different and often indicate disapproval of a post's premise rather than attacks on you. They don't mean it's a bad question, just that others disagree.
Ideally this would be displayed only to low rep users or users with low Meta participation, and show as a non-modal information box before they post a comment on their own question containing some reference to downvoting to try and catch the "Why downvotes?" comments. This would be similar to the "Hey, your title looks subjective and is likely to be closed" notice.
I noticed the formatting help box is a nice format to offer this help:
Yes, users can manually explain this, but it gets tiring and it would be nice to have the system acknowledge this fact rather than leaving the asker stranded and confused until some good (non-sarcastic) Samaritan explains the system yet again.