Deployment. Even if the framework were more widespread deployed what happens if a non-framework user tries run your .Net application? Are there any Installers that auto-magicly detect the missing framework?
I feel kind of silly promoting my own blog but:
I have a few posts on the new Whidbey generic bootstrapper that will allow you to install any components that you need (.Net framework included) as well as links to the Everett bootstrapper which will just install the framework if it's not installed already.