Native applications are binary and can do all sorts of nasty things. Sure, this sandbox is supposed to be safe, but what if it's not? When an application is delivered over the web, one should really make sure that it wasn't somehow changed or sabotaged. Right now this is impossible. At the very least, this proposal would have to be implemented so we can trust what is being downloaded: http://news.ycombinator.com/item?id=2024164
Here is what I suggest: native libraries should expose their objects to javascript, which should do the majority of the work. Kind of like PhoneGap does on the phones. These native libraries (like OpenGL, say), should be served from cdns over httpc:// and the user agent can verify that they are safe after downloading them.