Apps are a return to the walled garden -- the anti-Internet, if you will.
The data is not the problem, the communication medium is not the problem, the issue is the control over the distribution channel.
Yes, HTML is a big part of the internet, maybe even the biggest, but its not the only one.
If this were really the case — not just in a spec-sheet way but in a user experience way — why are all these companies making apps?
If webapps had the same payment/installation procedure, they'd take off like a rocket too. (Given HTML5's local caching and the like.)
For instance, Chrome Web Store offers a payment/installation for web apps, and it doesn't seem to be taking off like a rocket.
Steve Jobs even started extolling the virtues of Apple's ability to "bring subscribers" to digitl publishers, and going by their latest announcement, Apple themselves regard their platform as being worth 30% of the value of the content, even to those who would rather process payments themselves.
It remains to be seen how far consumers and creators agree.
Personally, my strategy is to create my product as a REST web service and provide some kind of default web interface, but let native clients use the REST interface to provide a nicer experience where applicable. I.e. the HTML interface is just one possible "view" to the service.
Why does my native app have to be the completely generic web browser native app when it could be a specific "web browser" custom tailored for my specific service?