IIRC Jobs specifically mentioned that the built-in apps couldn't have been built to the same quality if they were Web apps. But then he told developers to write Web apps. So either he had a "native for us, Web for you" policy or he was just stalling until the App Store was ready. I'm inclined to take him at his word, but considering RDF we may never know for sure.
Or door #3: steve jobs thought 3rd party apps would do more to ruin the experience than to improve it, and all-in-all users were better off without them. Given his control freak tendencies, I'm inclined to believe that last option.
At the time that he said that, did Jobs indicate that web apps on iOS would ever be given hooks into the accelerometers, or GPS, or mic? Because if not, what would the point be?
I remember reading somewhere that they /did/ try to build some of the iphone 1.0 apps as something akin to dashboard widgets and found that the hardware just wasn't quite up to the task, and they were forced to build them as native apps for performance reasons. This says to me that ideologically, they were convinced that the osx dashboard widget method of development was the way to go, but the reality of mobile hardware, combined with their even stronger ideology of responsive user experience made them go native.
It's funny that you pin it on Jobs, who didn't want apps in the first place. Indeed, in 2007, Apple was telling developers to make web apps - http://www.apple.com/pr/library/2007/06/11iPhone-to-Support-...
It was user demand that drove the creation of third party native app development.