The author never fully answers this questions but by implication, the priests must have learned some way to make the metal less dangerous. It is obvious how the metal became dangerous during "the Great Burning".
Somehow the metal was poisoned or became radioactive. It's important to note that this story was published in 1937, before the first atom bomb was built. This suggests some other kind of poisoning , perhaps chemical, that the priests knew the antidote for and were able to "cleanse" the metal before others used it. Benet does say the Hill People, of whom John is a member, did "not forget the old writings", implying one or several of them were able to decipher how to make the metal safe.
It never said the reason exactly but it seems as if because they are chosen. Just like he was chosen to be able to get farther than everyone else.