The command set mentioned earlier would be used to read from or write to the UART hardware. The other side of it would be some dedicated hardware to manage the UART protocol which includes logic, buffers and line drivers and the sorts. This hardware takes care of one side of the equation (communication with your PC). Once those drivers are loaded, this would specify a command set that your PC can use to query the chip.
The responsibility of this hardware is to tell your PC what it is (using some identification information) such that your computer can load the right driver for it, and also to manage the data transactions with the PC there-on after - look up USB endpoints for a better explanation of these processes.
The FTDI chips implement the USB protocol stack.
