I'm trying to learn more about momentum and I'm a little confused. Based on my understanding, in an isolated system, total momentum is conserved in a collision. Today in class the professor went over an example of a car on a ferry driving from one end to the other, in the opposite direction of the ferry. According to him, the total momentum for the system was zero in this case. I understand why total momentum is zero in a collision: because the objects come at rest. But in the example both the car and the ferry are moving (the goal is to find the ferry's new velocity as the car takes off).
So my question is: Is total momentum always zero if two objects are in touch with each other and are applying the same amount of force (but in the opposite direction) to each other? Also, the water applies the same amount of force to the ferry (again in the opposite direction) but how come it's not considered in our "system"?