I have a breadboard 8Mhz 328 built using the same reference page and my FTDI cable seems to have the same coloured wiring as yours except that I have a label on mine with Orange Tx and Yellow Rx. To be honest I can't remember if that means those are the FTDI usage of the wires or if they are the crossed-over labels. I can't recall having any problem programming the 328 with the cable.
In case you are interested I have two sets of pins on my 328 board for connecting the FTDI cable. One set doesn't have a pin for RTS so I can read the 328 without causing it to reset.
...R