Guests at Great Adventure have so many places where they could throw things at trains. The exit to Dark Knight runs parallel to a section of track. If someone wanted to they could easily throw something when a train was passing. Superman: Ultimate Flight's queue runs entirely underneath the ride and the first drop comes very close to the path. It's not really easy, but someone could do it. The entrance to Bizarro in the center of the cobra roll is pretty much begging for someone to throw something at it. And out of all of the rides that are easy to throw stuff on, the one time it occurs is when someone throws change while on El Toro.
The way I look at it, anyone who knows anything about rides and safety isn't going to throw anything because we aren't stupid. The people that don't know about ride safety would be too scared to throw something at a ride because they don't know what might happen. Movies like Final Destination 3 lead people to believe that a video camera could derail a speeding, multi-ton train. The amount of people who believe this stuff is incredible, which is why it doesn't happen. I'd be willing to bet that people who would throw something are turned off by the idea of something breaking and people getting hurt or killed, but most likely people getting hurt. As specific as my idea was, even the "coolest" kids don't want to hurt someone.