The article misses one key point in favor of web-based applications -- you don't need Apple's permission to write one. Writing an iPhone app consists of agreeing to an EULA to get the SDK, then writing the app with proprietary APIs and arbitrary restrictions (you can't call this function; you can't use a language that allows code modification at runtime[1]), and then finally gambling on whether or not Apple will approve it. If they don't like it, all your work is wasted.

If you write a web app, you have none of these problems, and you don't have to share your revenue with Apple.

[1] As anyone knows, this is not technically possible. Are config files or preference settings "code"? Why not? And what about languages that allow putting shellcode on the heap and overwriting the saved instruction pointer with its address... like, say, Objective-C?