It's about how useful those atoms are in a certain arrangement. Everything is composed of basic elements and we all know that. That doesn't mean that everything can be instantly devalued by saying "it's just a bunch of atoms!"

If we take a useful arrangement of element and transform it into a useless arrangement without a good reason, what we've done is a net loss for whoever or whatever found the previous arrangement useful. The atoms can't be destroyed, but their immediate utility can.