[jasongullickson]

I don't know everything about how phonegap works, but I gather that you embed your javascript code in the application (as opposed to downloading it from a webserver) and this code is loaded and run by the phonegap host app code when your app is launched.

Imagine a poorly written application that inadvertently allows it's javascript source to be modified by a third party. This third party then would have the ability to exercise any of the api's exposed by the phonegap host process. Again I'm not intimate with the functions that phonegap exposes, but I can imagine a few parts of the native SDK that you wouldn't want intruders probing on your phone.

This is why Apple doesn't allow all of the SDK's tools to be accessed via javascript running in the browser (Safari) they provide. They do expose some native controls (as can be seen on iphone optimized websites and apps) but there is a limit and I imagine this is one of the reasons.