Here are a couple of pictures of the Rhode Island Avenue Metro stop. The first one gives you some perspective on how high the platform is off the ground. The second one shows the area where the two boys were throwing the rocks from.
As you can see from the track bed for the commuter and freight trains, there are all sorts of rocks kids could pick up and throw at the train.
I'm going to send an e-mail to Metro about what happened and see what type of a response I get.