This answer from Ven. Dhammanando is so precise and on target that I'm reluctant to post what I have been thinking, because it doesn't add much. But here goes:
Seems to me that all the external stuff (throwing rocks, etc.) could stem from all kinds of different conditions, and we're all going to face those types of circumstances as long as we're bound to samsara. So there's probably not much point wondering why bad things happen to good people. It's just life.
But the point is that in the moment those things are happening that we perceive as "bad," we have an internal experience, followed by a reaction that usually is so quick we don't even notice the connection. But that reaction is our own, and it is possible to react from wisdom rather than from ignorance. So when the Buddha told Angulimala to bear with it, I think he was speaking to Angulimala's method of reacting to vipaka. Whereas previously, Angulimala might have reacted to that "bad" situation by killing the rock-thrower and chopping off his finger, now Angulimala could react with metta.
But the notion of kamma still works fully well. It just means that kamma and external circumstances might not be bound together in the way we sometimes think they are. That's my understanding, any way.