Quoting a Deseret News article:
But perhaps what I found most concerning was the musical’s core message and what it seemed to imply about religion in general . . . So essentially, “The Book of Mormon” team started writing this musical from their position that there is no such thing as absolute truth. There are subjective truths that help you lead a better life, but as for the religious stories and miraculous experiences that a religion is built on, these are too unreasonable for an intelligent person to accept as literal.