The difference is fidelity. Simulators strive for real-world emulation. Educational sim games abstract away a lot of details and will have lower fidelity. The purpose is often to get familiar with basic cause/effect within an environment in which the player can win or lose and experience a variety of situations. Sim games also tend to contrive the virtual world to present conflict and entertainment.
I build CyberCIEGE, which most definitely is NOT a real-world simulation of network security. However it is a constructive management simulation that confronts players with choices that lead to learning. And, for at least some students, it is fun.