As science journalist John Horgan writes, quantum theory is "science's most precise, powerful theory of reality. It has predicted countless experiments, spawned countless applications. The trouble is physicists and philosophers disagree over what it means, that is, what it says about how the world works."
At the core of the disagreement is what matter consists of at the quantum, or the smallest, level. At that size, matter's properties change when we try to observe it, even—amazingly—because we try to observe it. That's led to over a century of frustrated efforts to understand exactly what the fundamental "stuff" of reality is. It's not that these tiny things aren't real; it's that we can't figure out what they're like.
At the same time, quantum theory has proven explanatory power.
A theological parallel is the Trinity. We can't comprehend exactly how the Godhead functions, but that doesn't mean it's not real.
As C.S. Lewis wrote back in 1952, if Christianity is true, it would be "at least as difficult as modern physics."
And, we could add, just as rational.