If a user is confused about all the choice they can just stick to the software Apple and a handful of popular vendors provide. It stays simple by the fact that they can just ignore all the other choices.
To actually make things simpler you've got to make it easier to choose. When you download a desktop app, you've got to trade off between, "is this app useful to me", and, "will this app break my computer". Since apps on the iPhone are sandboxed, and are garunteed to uninstall cleanly, you don't need to worry about the second question.
Also have a look at what Microsoft are doing with permissions in .Net, they are slowly making it easier for Windows applications to be sandboxed. In a secure Linux enviroment, it is standard practice to give different apps their own users, with tailored permissions, eg the www user.