It is my understanding that people aren't supposed to be generating rep from community wikis as that is our holding place for the subjective and lists and whatever. However, you are still allowed to post bounties on these questions. I don't really have a huge problem with it but it seems odd. I know that it is singled out specifically in the FAQ, but I am having a hard time understanding the underlaying reasoning. I was just hoping somebody would be able to explain it.
The fact that Community Wiki posts do not accrue reputation is merely a side-effect of what Community Wiki is really for. I've been meaning to write something more detailed on this but haven't been able to find the time.
Community Wiki means, in Wikipedia-like fashion, that (almost) anybody can edit the post, and thus it is a collaborative effort. No reputation is given because the post is owned by the entire community and not the original author.
But this process of gradual and constant editing is intended and expected to happen over a long period of time. Bounties are short-lived (7 days) and intended principally as a means for drawing attention to a question. If you couldn't start a bounty, there'd be no way to get a Community Wiki question featured. And as you can see in the molecular gastronomy question (which I'm guessing is what prompted you to post this), the system works just as well - the question received a much more detailed answer than any that had been provided before the bounty was started.
Over the relatively short bounty period, Community Wiki status isn't all that important; it's unlikely that an answer is going to receive that many edits within 7 days, and even if it does, you could argue that the originator of that answer was chiefly responsible for helping to get the bounty "resolved."
Community Wiki questions are just a way of saying that the question isn't expected to have a single clear answer. Rather, it might have an encyclopedia-style answer (like wikipedia) or perhaps a list of answers. But bounties have nothing to do with acceptances - they used to but that wrinkle was thankfully ironed out - now anyone can start a bounty and the bounty-awarded answer does not have to be accepted (in fact, there may be many bounties started on a single question, each awarded to different answers).
If all of this sounds too handwavey or complicated for anyone then just think of it this way: Bounties work outside the normal reputation system. They're immune to the 200-per-day reputation cap and they also can't be undone. I'm pretty sure you also keep the reputation even if the question/answer is deleted. Basically, bounties are just "special" and are immune to Community Wiki status like they're immune to everything else.