USB has nothing to do with root. You use the cable the same way with root as you use it without root, unless the particular app you're running needs root - then you'll be asked (by the SuperSU or SuperUser app) whether to give it - the app - root. If the app uses the USB cable, then it's using it with root.
Root gives the app requesting it administrative access to the operating system, it has nothing to do with USB. USB isn't implemented, it's part of the hardware of the device. If it's "implemented" anywhere, that would be a combination of places in the OS.