Because web-based apps don't have a good user experience. Even a web app embedded inside of native app feels bad. Maybe it's something about WebKit specifically

Because web-based apps don't have a good user experience. Even a web app embedded inside of native app feels bad. Maybe it's something about WebKit specifically that feels bad, but there is a very noticeable difference between a web app and a native app. Part of the issue is the thread model. Touch events come in on the app's main thread, and then those touch events get dispatched on to the JavaScript thread, and then the JavaScript thread needs to dispatch to yet another thread to render. It's just impossible to achieve native-level touch interactions in a web-based app. And then there is there is the polish level. Apple has spent god knows how long polishing each and every native interaction. All the animation curves are perfect. You lose all of that polish when you build a web app.