How to run Arduino-on-breadboard at 3.3V and still have USB communication to PC
The supply voltage of the FTDI chip will usually be 5V.  However the communication I/O voltage can be set separately.  For example on the FT232R there is a VCCIO pin which needs to be pulled to the desired I/O level.

If your FTDI board allows you to change the voltage on the VCCIO pin then you could connect it directly to the 3V3OUT pin and the FTDI will work correctly with the lower voltage 3.3V compliant I/O.

If the FTDI board is fixed to 5V I/O then you will need to use some form of level translator.