Before watching Burns’s documentary, I had a higher opinion of Muir. Burns turned him into the patron saint of animism, a worshiper of creation rather than the creator; this, despite the fact that Muir had committed the entire New Testament to memory.
My take, from reading Muir, is that he became a nature-worshipper, in the mode of the Transcendentalists like Emerson. He had a terrible upbringing under his father, who was mean and rigid. It left him with a bitter misunderstanding about the Christian religion. He may have memorized the text of the New Testament, but when it mattered in his upbringing, he did not have the experience of a loving Christian family. He did not have the consolation of the faith, only the words. Very sad.
One less severe example of his upbringing that I remember was that his father thought all his scientific curiosity was a big waste of time. He wanted to build a clock, and his father told him he could not waste any of his free time during the day on something that useless. The next night, like around 2:00 a.m., his parents heard a little noise downstairs, and came to investigate. Muir had forced himself to wake up so that he could work on his project, and he was going at it. His mom intervened that time with his dad and said, “you did tell him he couldn’t waste daylight, and so he is not.”