Our modern understanding of reality is based on some fundamental concepts: that the world around us is tangible, that the theory of relativity holds, that cause and effect works as we'd expect, and that humans have free will. But take quantum theory at face value, and it turns out the four can't co-exist together.
I think there is a misunderstanding between the macro and the micro. Yes, the rules at a certain size level of reality are radically different. Think of it like this: water in a pot if left alone will be still, but if you apply enough heat it boils. The moment before it boils, the water is still, this minor change in state is like the size change. Yes, at a subatomic level, cause and effect can be meaningless, but once you cross the threshold our macro physical laws are in effect and cause and effect assert themselves.