I have this conspiracy theory that I half believe: it was all a ruse.
Apple knew that there would be huge pushback against a walled garden appstore with Apple in absolute control, and huge pushback on them taking a 30% cut. So they started with "just write web apps". But of course, they also inexplicably made the first iPhone 2G only! Flagship phones that shipped many months before the iPhone had 3G. Why cut that particular corner, and not any others in their otherwise $$$-is-no-object new wonderphone?
You can do a much better job hiding low bandwidth and high latency in a native app, especially since app assets get downloaded once (probably over wifi) at app install time. So by essentially making app developers beg for access to their native platform, they radically reduced the anger at their wildly locked-down appstore and their 30% cut.
And it seemed a little suspicious how quickly they were able to deliver a 3rd-party SDK and developer documentation.