The config file /etc/xdg/user-dirs.conf (overrided by ~/.config/user-dirs.conf) allows to you to enable or disable the automatic folders (re-)creation. If you set in it enabled=False, either globally (in /etc) or for your own user only (in ~), the special folders (such as Documents, Downloads, Pictures etc) will not be re-created every time at login anymore in case you previously have deleted or renamed them.
Original Thread: https://superuser.com/questions/223918/ubuntu-permanently-remove-videos-and-public