There are things that are better done on the desktop. Take Spotify, for example. One of the key to their success is the fact that they keep bandwith costs low by using peer to peer technology.
I've done some research, and found that on average, 80% of the music I listen to on Spotify was coming from peers rather than from Spotify's servers. If I'm anything like an average user, that means that Spotify may be cutting its bandwith costs by something like 80%. That would be impossible to do as a web app, and web-based competitors face huge streaming costs indeed.
But seriously, I don't think Spotify could be the great app it is if it were a flash app. Can you imagine yourself running a tab in your browser with an app like Spotify inside and your fans running full-speed on?