They are example questions after all, aren't they? Why do they affect your reputation on Area 51?
Even if an example question is downvoted, why punish the user with -2 reputation for it? It's excellent that example questions get downvoted in the definition phase; otherwise, we'd only know what kind of questions should be asked and not what shouldn't.
So why have votes affect a user's reputation on Area 51 when downvoted questions are vital to the scoping and true purposing of a site? I feel no reward or punishment is necessary for helping identify a proposal's actual legitimacy/validity.
This will also help people who really do understand the site proposal system get their privileges faster.
Is Area 51 reputation similar to Meta's, in that it's not really a measure of anything but whether people agree or disagree with you?
EDIT: Just some more reasoning. If we remove the gain/loss of reputation from example questions, it empowers our experienced users, the ones that understand the system of proposing the site more than any of us, because the only other source of incoming reputation would be to get followers on a proposal or to refer people to another proposal. I think this would be valuable on Area 51. Sure, it would reduce the amount of users with higher privileges, but it puts the ones we can trust more with the system in power.