The crucial features of paired (transistor) NOR gates which make a flip-flop work are:
- Propagation delay. Simulink models things instantaneously by default. If you want to model propagation delay, you can either add a Transport Delay or Time Delay block, or you can use Simscape Electrical.
- NOR gates are built by pairing transistors that have a nonlinear behavior across a range of input voltages, to get a bistable output value of something-near-GND or something-near-VCC based on the inputs received. Simulink models a NOR gate as a simple logical operation, where either input being true produces an output of false and neither input is true produces an output of true. You miss the analog behavior, which is also relevant to transient behavior of the transistor-based real-life NOR gate. To model that behavior, you would need to feed the transistors' (or transistors' and resistors') nonlinearity models into Simulink (perhaps with a 1-D Lookup Table, and you could get away with something simpler for a resistor since it's really linear), or, again, you can use Simscape Electrical.
What are you trying to do that requires you to twist NOR gates together to make a flip-flop, or were you doing this for curiosity's sake?
