In every one of those comparisons, the new technology offered a fundamentally new potential that the old technology lacked. Even in 1965, people could appreciate automation. Even in 1988, people could see the potential in putting a computer on every desk. Even in 2002, people could see that web apps were accessible wherever the web was accessible, instead of needing to be installed separately on every computer where you wanted to use them.
What do HTML-based apps offer the user that native apps don't? They're easier to create and update, and they offer an inferior user experience. It may be an exciting new paradigm for developers, but from a user's point of view, it's just a cost/quality trade-off. The only distinction that is meaningful to users is installed app versus web app.
> They're easier to create and update, and they offer an inferior user experience.
No, they're not. Good web apps have never been easier to create but what they offered was extremely easy distribution. What Apple did on the iPhone was make distribution almost as easy as going to a web page, knocking out HTML-based apps best advantage.
If you account for the requirement to reliably maintain per-user state, native apps pull into the lead. In most cases, they can store state on the device with no extra work from the user, whereas web sites require tedious signup to remember even the most trivial personal settings.
Also, don't discount the joy many consumers get from shopping and owning things.
Seems like the article is about HTML5-based mobile web sites vs. native apps, not HTML5-based-apps vs. native apps. (It generally fails to define what it means, but I'm guessing they mean web sites given the reference to Apple telling developers to make HTML5 apps for things they won't let into the store. At least on iPhone, not-in-store equals not-an-app.)
Lower cost of development and lower cost of maintenance translate into more (and better) services for end users. It's unlikely that web apps are going to compete with "sovereign" apps on a phone like email or an RSS reader. But for a niche or transient application (like say, making a flight reservation or looking up your order status on a web site) the web apps probably are a better experience.
This has always been true on the desktop as well, until recently - you wanted a local email client and text editor, but you were fine using the web to access Wikipedia. (That's changing now, of course.) It's not sexy but _most_ web services / sites are transient, not sovereign, software and will likely translate better to a web app than a native app.
What do HTML-based apps offer the user that native apps don't? They're easier to create and update, and they offer an inferior user experience. It may be an exciting new paradigm for developers, but from a user's point of view, it's just a cost/quality trade-off. The only distinction that is meaningful to users is installed app versus web app.