I plan to use the workspace in order to manage different volunteer organizations that I'm a part of. For example, I am a Cub Scout Leader and would like to put information in a workspace for others to get to. But some of that information is for leaders, some is for the parents, some is for the scouts, etc. If I make 1 workspace called Cub Scout Pack and put all the documents in there, then parents may be able to get roster information on other families which I don't want. So I'd like to create sub-folders (assuming you can put separate permissions on them) for Leader, Parents, Scouts, etc. Not to mention putting pictures out there. Mix a couple hundred pictures in with all the other files and ... well, it just doesn't make sense to do that.
Optionally, I could create 3 different workspaces to do the same thing (assuming I don't want nested folders, but I do). Multiply that by every organization I might do this for (scouts, hockey, soccer, American Legion, etc) and the number of workspaces could become too unweildy.
Folders are used everywhere for normal organizing skills and should be here too.