And yet web browsers support a far larger world of applications than .NET has. Consider that every website is essentially an independently-developed HTML-based application; do you think there are more of them than there are .NET-based applications?
Those small incompatibilities may be annoying, but they're a small price to pay for the otherwise easy development and broad reach of the HTML+JS+etc platform.
The greater the diversity in the market, the more appealing HTML5 becomes. It's bad enough supporting two platforms but 3-4 is going to push a lot of shops to the browser. Unfortunately, both Apple and Microsoft have significant incentives to make sure the browser experience is always inferior to a native app.
If this becomes the standard, like I suspect it will, one of the biggest losers will be companies that run big app stores.