The difference is that iOS allows Mobile Safari to turn memory areas into code pages, which is what you need to do to JIT JavaScript. It doesn't trust other apps not to be able to exploit that somehow, so UIWebView is not allowed to do this.
They would rather do that then open an exploit possibility. As a user, I prefer that trade-off. It would bother me if I relied on PhoneGap or something similar, but in practice, the performance really isn't that bad.
