USB separation in RF design
I definitely would apply galvanic isolation, for the reasons Steven mentions. Especially ground loop currents can create offset voltages over all your circuitry.  

It may sound logical to have the isolation on the UART level, because Rx and Tx are unidirectional, but you can also have the isolation on the USB. If you want to go that way, don't DIY this, buy a commercial product:



This one is USB2 Full Speed and costs 34 EUR.