I would certainly agree that if we are talking about programming you cannot really expect everything to end up being web applications. As an extreme example I am working with SIM cards and sometimes have to write code in pure Hex. Why? Because in some occasions is much faster since the tools used are not perfect. The same concept that if you had a micro-controller where you couldn't write C code but you had to write asssembly code you would do so. Maybe it is not cost-effective to have a compiler/program to support C code for example. Maybe your company will develop it at a later stage.
Web apps have some downsides and limitations. Speed was already mentioned. Loading speed for your browser might be another. Making Need for Speed a web-app instead of a desktop application would be ridiculous. You get my point. It is nice to be able to run a program as a web app, but if you are actually going to use it everyday then I think you would prefer it as a desktop app. MS went towards the web app with Silverlight, but I don't think they would actually stop having MS Office or Visual Studio as desktop apps.
But of course both have their place. Web apps are mostly suited as small apps, that you might not use a lot of times or for apps that are tied with the internet.