There was, is, and will be controversies over certain books for Christians. There was a big controversy over Harry Potter, as to whether it was okay for kids to read books that glamorized magic. But when you really get down to the message of stories, many of these books aren't bad. In fact, I would argue that one of the children's classics that has been accepted for decades is actually far more anti-Christian, or anti-religion, than books like Harry Potter. Though I have not read a biography of Baum yet, I am guessing at this point he was cynical. Now, I have not read his books, but I am going by the film.
The spiritual journey is an old, old metaphor. One very popular and early book is Pilgrim's Progress, in which the character takes a journey to find Heaven. Along the way he meets characters that are allegorical, for instance Gossip, Disbelief, etc. As I read the book a few months ago I could not help but think of the Wizard of Oz. As I thought about it more I realized Baum, satirizing the spiritual journey, makes God out to be the Wizard--a fake, a charlatan whose only power is by scaring people. The message is that a person should believe in oneself, enjoy worldly pleasures (of home), rather than think on some other paradise like Emerald City.