arusr:
Isn't the Arduino using the same FTDI chip to program? I guess not...?
The Arduino UNO uses a small ATmega processor to do the USB-to-Serial job.
Is your DTR line connected to the Boarduino reset line via a capacitor? If not you will need to do a manual reset. Hold down the Reset button (add one if you left that out) and click on the upload button. When the Receive LED blinks (add one if you left that out) release the Reset button.