The question could also be rephrased. I've got a software application that requires a USB dongle. It works correctly when running at the console of the remote machine, but when connecting via remote desktop it does not seem to work.
I've seen this behaviour before a few times and wondered whether or not it is possible to block access to the usb ports, and if so, it should be possible to allow access.
For a quick fix, run remote desktop with the /console or /admin switch, that will connect to the console of the remote machine, and should then have access to the dongle.
Check the Local Security policies of the machine for device access policies.
Have you tried unplugging and plugging in the dongle while connected with Remote Dekstop? It may just need to install the drivers when connected as a different user.