The win of webapps was always that they didn’t require any client-side installation process: no installer to run, no arguments with sysadmins about “approved” software, and no hassles for developers trying to update thousands or millions of client installations. To cite my own experience, I wrote a Java Swing client application in 1999, and in 2003 I found myself assigned to rewrite it as an IE-only webapp, a huge step backwards in usability and compatibility, but so much easier for customers to maintain that it was a no-brainer. Not having to drive out to client sites to debug botched installs or unanticipated network hassles got me over my aesthetic qualms pretty quickly.
With the iPhone and the App Store, many of these problems go away. With the filesystem abstracted away, many of the installation hassles disappear: click “buy” or “download” and the app is on your device, ready to run, and impossible for the user to mess up by moving or deleting needed files. Updates are trivial to perform, and a red badge on the App Store makes sure the user always knows that he or she has new features or fixes available.