You are correct that passive learning--sitting and watching--is not good enough. But some of these simulations are interactive, they provide varying levels of feedback. There is one of a frog that is quite good:
http://scienceman.org/dissection.html
Check out the one called Froguts. For some strange reason people seem to think that I believe a simulation is an acceptable substitute for other learning activities, even though I haven't said that. All I have said is that it depends what the intended outcome is. That will determine the best teaching method.