Better way is to use a Logic level, Low Rds, P-channel MOSFET between power and FTDI Vcc pin.
Bring the uC TX to the FTDI low before turning off the MOSFET (with a high signal on the MOSFET gate) so that power from the TX pin does not keep the FTDI chip running via internal leakage currents.
Here is a circuit I've used before, D4 blocks current from the CPUs Tx pin and stops it powering up the FTDI through the internal ESD diodes.
This is only required if the CPUs Tx pin remains at a high state, if you can detect that the USB is not connected you can either drive that pin low or make it an input. In either case it won't power the FTDI.
Speaking of Schottky diodes, just use one between the USB power (including the FTDI chip) and the main processor. Simple as that - the primary power for the FTDI is only there if the USB interface is plugged in (including a passive charger with no actual USB interface).