Why does the potentiometer have no effect on the output voltage here?
You have the pot connected to the output.  The flip-flop changes its state based on its inputs, not the output.

It's hard to even guess what you think was supposed to happen.  All you are doing is changing the loading on the output.  However, with about 920 &Omega; lowest impedance you are putting on the output, it should still largely stay high or low according to the flip-flop logic.