I don't think this is true. I'm not a Christian and I loved his books as a kid. Tolkien and Madeleine L'Engle wrote novels in a similar vein (that are also excellent children's books). Some fiction is full of cliches and thin characters but, surprisingly, this ends up working in its favor as it takes on a mythical quality.
I also like moral ambiguity and morally complex characters but good luck getting a child to sit through The Brothers Karamazov.