Well, the film is all about faith and the miracle of faith.
The lead character makes the distinction between just-is people and people of faith. The just-is people only see what is, they have a mechanical view of the world. They ONLY see numbers and so on. THe other people, people like her, see the mystery and wonder in life.
The story climaxes with a dull world. Children aren’t having fun, toys don’t work and so on, until she gets faith. Then the world is coloured. The main love interest goes from a just-is person to a person who believes, and the whole world is transformed.
Now the story doesn’t say faith in something outside of us is a good thing. The film seems to stress that faith in oneself, that one can so things beyond the mere ordinary and that that faith is transformitive in our lives.
Faith in oneself can be just as deluded as belief in things outside of oneself - as we’ve all encountered in other people, if not in ourselves. But it may be even worse: for if you believe in gods or other things outside of yourself, you believe in something that *may* eventually prove itself or not. Your belief implicitly is in something that isn’t under your entire control. But if you have a deep and abiding faith in yourself, there is no such ‘brake’ on your beliefs at all, for there will be no difference between the believing thing and the thing producing the belief.
It seems one must have faith in ‘facts’, and drop the faith in oneself. One needs rather knowledge of oneself - knowledge of one’s skills and limitations. One then has faith with reason in one’s skills.
The Wonder Emporium can only be animated in a ‘nice’ way because of Mr McGorium himself, making sure there are no man-eating tigers that will be animated in the vicinity of the kids, for instance. So *indirectly* - without quite meaning to - the movie does indeed suggest to the sharp mind watching it that the faith is founded on the owner of the shop - they just don’t emphasize it, but there McGorium is.
So I can see why someone would claim it’s somehow, indirectly supporting faith in a god - or maybe faith in weird guys wearing loud suits who claim toys won’t work unless you ‘have faith’. Because, to summarize (1) The moral is supposedly having faith in yourself. (2) But everyone already knows that faith in yourself, in some general way that lacks support, isn’t much good. (3) So the mind naturally turns to looking for a more likely source for one’s trust and faith. (4) And that’s the ‘authority’ present.
A rationalist might want to champion the ‘just-is’ folks after all. Maybe however it’s just not easy to make being a just-is person very appetizing. Witness the difficult reception of the movie The Golden Compass. It seems to me that the children are a parallel to the just-is people of the Wonder Emporium.