Semantically speaking, there's no difference. Pragmatically, it's the way Kris describes it.
A Yes/No question (the kind that doesn't start off with a Wh-word) can go either way, because if you're asking whether it's raining, you're also asking whether it's not raining. The answer to one gives you the answer to the other. So, semantically speaking, there's no difference.
However, language is a lot more than semantics. Language is a natural, evolved, phenomenon, and like anything evolved, it doesn't waste anything redundant. So if there are two ways to do something, people will tend to find uses that take advantage of the difference.
In this case, it's an invited inference about the expectations of the speaker; or, depending on context and intent, an invited inference about the beliefs of the speaker about the listener's expectations (pragmatics can get very complicated at times, and shades off into rhetoric, politics, and religion).
Neither one of these, by the way, are grammar -- that's still a third part of language.