First, understand that this happens only on this meta, on Meta if you will. On per-site metas there is no independent rep and therefore votes have no effect on you other than emotional responses you may have.
Second, a feature request on Meta is a bigger deal. If you are the 4000th person to suggest that comments should be mandatory when downvoting, or that downvotes without comments should cost more, or any of other dozens of feature requests to solve the problem of commentless downvotes, then you are demonstrating that you don't really understand the history, culture, and mechanisms of the SE family of sites, and reducing your reputation seems like a fine response to that. If you are the first person to suggest that when two users post similar (almost identical) fact based answers to a question like "how long does it take to get from Paris to London by train?" or "which of these three sort methods is fastest?" or "what is this low plant with white flowers" that one of them should be forced to delete their answer, because they were obviously copying, then you are again demonstrating that you don't understand how these sites work or what they are for, and you're going to get downvotes and lose reputation.
I downvote FRs when I don't just dislike the suggested feature, but the question shows that the person cannot possibly have given the request the thought it deserves. If I disagree with a FR but think it shows thought and is generally aligned with the site, I will just upvote an answer that says "I don't support this idea and here's why." If such an answer doesn't exist I'll write one. I understand some people just see all FRs as polls and up/down vote to indicate what they think, but I don't believe those people are the majority.
When FRs get downvotes we often soothe the asker by saying "downvotes on Meta indicate disagreement, not quality" and that's sort of right. But you get more downvotes if your idea is actively wrongheaded or has been suggested many times in the past.
Finally, there are a number of logic holes in your post. You assume for example that Meta voters will downvote a feature request just because other people are doing so, and apparently believe that happens more on Meta, and therefore we should change the mechanisms to guard against that. You also seem to think that whether or not you gain or lose Meta rep is more important than whether or not your feature request is accepted. I've suggested a lot of things, and got a lot of rep for my suggestions, but they haven't been implemented, which makes me sad. The rep is no consolation, believe me.
As for what you should do if you get a lot of downvotes for a bad suggestion, I would try in this order:
- edit it a little so that it is less objectionable. I don't mean change "ban" to "encourage" but maybe soften it a little, or just add more explanation
- if you haven't earned the Peer Pressure badge, and you are in no danger of a post ban, delete it for the badge
- if it is hugely downvoted consider asking to have it dissociated from your account so the rep loss doesn't hurt you
- most importantly, understand why people reacted quickly and strongly. Very negative questions are not shown on the front page, so getting a lot of downvotes will happen very quickly in most cases. Did you use inflammatory wording? Proceed from assumptions that were so wrong they offended some people? Suggest something that's been suggested many times before? Learn from it.
The smarter move is what you've done here, which is to ask about a feature before suggesting it be removed or changed. Your underlying logic is right, and you can see that in the lack of independent rep on the per site meta sites. But Meta is special and this is one of the ways that it is special. Rep here is real. And the rules here are not like other places, and not all written down. And not everyone behaves the same or follows simple and logical published rules. That's just how Meta is.