1. The dongle is an option for people who don't have regular internet access (for security reasons, bad connection, etc) who don't want to have to keep a DVD in the drive to keep X-Plane out of demo mode. There is no scenery on the USB dongle--it is just a DRM unlock. Digital download requires a regular internet connection (about every 2 weeks) to authorize DRM & keep you out of demo mode.
2. Pro license is required if you are using X-Plane in a commercial manner--to make money of any sort by using it. It also has additional features as listed here:
http://www.x-plane.com/pro/
3. You only need one license per machine, not per user. In your example you would only need 1 license for 1 computer.