Problems connecting an Arduino Uno to a Commodore 64 Joystick port
As far as I can find, the atari control port and game pad are active low connections. A pin is left open for a high, and pulled to ground via a switch to register as a low or triggered. Your board needs to pull the line low with a relay or possibly a transistor or mosfet.
You may be able to pull it low via a digital pin, but you would need to ensure that at the very least your arduino board is tied to the same ground as the control port.