Pin1 of the FTDI adapter must not be connected to reset of the Arduino - this pin goes low when the serial port is opened, and would hold the chip in reset, preventing the bootloader from running. You need to connect one side of a 0.1uF capacitor to reset, and the other side to the DTR or RTS pin of the serial adapter - this and the 10k pullup on reset form an RC that converts the high to low transition into a low pulse, which resets the chip but then allows it to start, the bootloader runs, and it can upload the sketch.
See the section of the Nick Gammon guide starting with "We can disconnect our breadboard from the Uno we used to program the bootloader, and using hook-up wire, connect it to the FTDI cable like this:"