(I'm a lawyer, but I'm not your lawyer, and in any event, I've got no copyright experience. And this isn't legal advice, it's just arguing on the internet.)
Commercial use is usually THE factor that swallows the other three. And in this case, you could pretty easily say that both factors 1 and 3 weigh against GoldieBlox--the purpose of the use was commercial AND they took substantially all of the work, including the "heart" of the work.
As for the inspirational message, I'm pretty sure copyright is supposed to be message-agnostic; otherwise, I'd think you'd run into First Amendment problems.
I think the question is the one @blambo raises: what happens if it's Ford, or Chevron (or Wal-Mart, or Rob Ford) repurposing a song you like for pure advertising purposes?