Simon, I would totally agree. I think most users perceive desktop applications to be more complex because they feel that if they know how to use a browser, they should automatically know how to use the web application that it presents.
In a way this is good because it encourages developers to make interfaces as self explanatory and accessible as possible. Intranet and to a certain extent intranet are in a much more exposed competitive environment than desktop applications. If a site doesn't work how you expect it or it is difficult to use, its much easier to go to the competitors offering than it is to swap desktop apps. For example, many people in big organisations have web access but do not the privs to install new software on their machine by themselves.
In an ideal world our web applications would self-customise their interface for the user depending on the users experience, know-how and so on. Many vendors are now adding desktop app style first-use help tips to users which acts as a training course on using the application/site. I think this is a really positive step forward for web applications.