I've been a member of SO for a couple of months, though only really active for the past few weeks.
It has only recently dawned on me (as a newer user) that "reputation" has nothing to do with the user's reputation as a question answerer or asker, but is indeed just a system measurement to determine what access/editing rights you have on SO.
And that realization only came through reading a number of postings here on MSO.
I don't think I'm more than averagely stupid as a website user (grin) so it must be confusing a lot of other new users too.
So why not call "reputation" something else instead that doesn't have an implication of human trust attached?
EDIT: I guess I'm thinking from the point of view of the forthcoming StackExchange when applied to non-technical users. I can envisage some confusion when a user with a "high reputation" provides an answer to a question and someone believes that answer to carry more weight as a result.
Yes, those sorts of inaccurate answers should be voted down but that implies there are enough users with enough knowledge to know the answer is inaccurate. On a newish StackExchange site, that might not be the case for quite a while.