Have you already forgotten that Apple first tried to sell the idea of web-apps to potential iPhone developers? The response wasn't good - almost nobody like it, and Apple was accused of trying to pitch a half-baked solution to them. Everyone wanted native access, a real API. And once Apple delivered, iPhone development skyrocketed in a way that surprised everyone (including Apple, I think).
And, in case you missed it, Apple still pushes HTML5 and web/cloud-based solutions too. They aren't so prominent to the public simply because developers haven't seized hold of them in the way they have with the App Store. I think the reasons are simple: 1) You can generally produce better/faster solutions with a native API; 2) The App Store provides a great mechanism for pairing developers with customers, i.e. making money, and it's relatively cheap (30% is a very reasonable margin for what Apple provides).