It's all about software delivery. Native apps, whether they be desktop or mobile based, will always pale in comparison to the simple act of clicking on a link, and immediately running the software - no downloads, no install, no headaches. Mobile natives apps can never provide this level of pain-free software experience. This is especially true if every app that can exist in the future needs to be moderated by a central authority (Apple). Mobile apps are not the future, it is the past, in new clothing.
Mobile apps are essentially a re-invention of the CD-ROM software era, in a new slick iPhone interface. Millions of people constantly re-downloading and upgrading the same software millions of times again and again. It's basically Windows freeware/shareware all over again. Some of these apps might have connection to a website, but it's just tacked onto an ancient software paradigm. Whereas when you starting building a web-based app, you already developing for that new hyper-networked paradigm.
In "the future", your web browser becomes the desktop, or the mobile UI, and the internet is the software. I promise you, in the long term, it does not matter how successful Apple, and previously Microsoft, are at deceiving you of this future. It will happen. And it is happening. Everywhere right now, there are millions and millions of developers building HTML5 apps, and every improvement to today's browsers is building our future software paradigm -- and it will not be controlled by Apple or Google.