I think India is a much more perplexing case; the faith was brought there by an Apostle and still has hardly made a dent in the subcontinent.
Probably all of the factors @Katsuobushi mentioned worked together, but none of them alone can explain why Japan is not a majority Catholic country today. Christianity was brought very late to the Americas, by an arrogant Western colonial power; it was harshly oppressed under the Roman Empire, which saw the belief in Jesus as Lord as a political threat; Christianity was always intolerant of other religions and wiped out European paganism; and it was brought to the island nations of Britain, Ireland, Iceland and the Philippines.
I watched a documentary about the Jesuit missions in Japan, and one of the Daimyo, Oda Nabunaga, was interested and tolerant of Christianity; but he was betrayed and lost his power, and committed seppuku. Perhaps it would have been different if rulers like him had lived and gained influence. Japan unfortunately never had a Constantine. [Although Constantine wasn’t even Catholic.]