You can do this by implementing the UnifiedFileSystem. Read the following whitepaper to get a clue.
http://www.episerver.com/downloads/Documents/TechNotes/EPiServer%204.40/Configuring%20the%20File%20System.pdf
You will then be able to set the rights on the folders in the upload directory the same way you do with pages.
You need v 4.31 or higher. No additional modules must be installed. It's shipped with EpiServer, but not enabled by default.
Thanks - I read about this in the book but I am getting conflicting information about which version it works in. The document you mentioned says it was introduced in 4.30.
Either way I had a suspicion it was the unified system but now Ive got 2 sources that confirmed it :)
/John