The cynics view would be because as the web app approach becomes less distinguishable from native apps speed, those web applications end up running as well on equivalent speed hardware such as Android and other platforms as they would on iOS, ceding some of iOS advantage in the richness and diversity of its applications.

However it should be noted most of the popular applications in the iOS app store are in fact games

The real reason is likely to be more to do with security around the js runtime, especially when UIWebView is placed in "wrapped" applications