To program the firmware on an XBee the six pins of the FTDI cable should be connected as follows:
1 (Black) - pin 10 ground
2 (Brown) - pin 12 cts
3 (Red) - This is 5V VCC even on the 3.3V cable. If you want to power the module from this cable you will need to adapt this power level down to 3.3V. (VCC will go to pin 1 but be careful to have the correct voltage.)
4 (Orange) - pin 3 tx to din
5 (Yellow) - pin 2 rx to dout
6 (Green) - pin 16 rts