As it's been made clear that voting on Meta basically means 'I agree/disagree with your proposal' and has no bearing on the quality of the proposal, it shouldn't have even a small affect on reputation. It's totally unfair that you can propose an idea perfectly coherently, but lose rep because a bunch of people disagree with it. This is likely to discourage people posting new ideas for fear of losing reputation.
Keep in mind that this is not an open source project. This is an attempt at a profit-making enterprise which accepts some suggestions from, and outsources many tasks to, volunteers. When you make a suggestion here, you are often talking to the fine folks who are paid to do the work -- and those fine folks reflect upon opinions here as they choose. They own the playground. If you find the swings too squeaky, the gate is in obvious view.
The rep system imposes a simple discipline: Answers get a lot more rep than questions. If you devote time to providing informative, thoughtful, answers, you will soon have far more rep than you can spend on the occasional highly unpopular question.
If, on the other hand, you expect to show up here and start telling the owners how things should work, your rep will dig for China in a hurry as the downvotes come flying along. And if you throw gasoline on the flame with the sort of sarcastic remarks in your comments above, you will only attract more of the same. Yes, it's a social control mechanism, along the lines of 'the nail that sticks up gets hammered.' But the definition of 'sticks up' is not 'posts unpopular ideas.' It's "ignores previous discussions, makes bombastic statements, displays a thin skin."
And, of course, you can choose to simply ignore rep. Are you really burning up with an urge to have deletion privileges here on meta?
It's totally unfair that you can propose an idea perfectly coherently, but lose rep because a bunch of people disagree with it.
Take an extreme example: let's propose that since we all have a reputation number, much like money (not strictly true, but go with this for a second), we should request that the SE team program gambling games where we can all gamble with our reputation.
Proposing such a feature would be a waste of time and energy of the participants of the site who (a) read the question, and (b) subsequently have to deal with it by answering or moderating. Losing reputation for such a proposal seems very fair, because it distracts everyone from more useful discussion. (See also, the Noise or Pointless close reason description.)
Generally speaking, unless there's some change or bugfix in the system that completely changes the face of a feature request, rehashing old discussions about it are a waste of time and we get a bit annoyed at having to talk about it again. You pretty much walked right into it with your other post -- please don't take it personally.
On the one hand, yes, voting is a bit of a popularity contest; but on the other, people here have a very good idea of what will work and what won't for the sites.
I think it could just be made clearer on meta that the up/down votes are for approval disapproval. For example the title tags on the up/down arrows don't say agree / disagree.
Also its a shame that features are still linked to rep on meta. I don't think suggesting unpopular ideas necessarily equates to being a bad member.
Reputation on meta is a score that combines the following:
Reputation = How much you participate + How much people agree with what you write
The more people agree with you, the higher your reputation on meta will be. If you have a low reputation, it's because you have 1) Not participated, or 2) written things people disagree with.