It is to allow you to use pin 0 and pin 1 without the FTDI chip over riding the signal level you put in.
If I understand your answer, it means that my AVR will be able to use its serial port on the PINs without being disturbed by the powered-on FTDI chip, correct ?
If correct, won't the 1K resistors "lower" the signal between AVR and FTDI when "talking together" ?
Regards,