KaiserPhantasma :
oxidation/rust or dust that's why I'm trying to cover it
Chances are, you are gonna get dust in there in any case. The shrouds on the ports are not sealed on the side attached to the MOBO, so you'll get some residue there regardless. It is just good habit to do a good cleaning of your system every 3-4 months anyways as dust on your mobo or heatsinks is probably 100X worse than in the USB ports. A nice 1$ can of air will do wonders to cleaning out ports, though.
Also, unless you have a... err... lesser quality mobo, you shouldn't have to worry about oxidation too much. And, once again, your case is most likely not an air-tight sealed system so, unless you want to want to hotglue each and every little crack and crevice, you will still have the "chance" at oxidation. Still, if you do want to prevent a build up of rust or such, just slip a usb connector into each port when you do a cleaning.