I count both CS Lewis and JRR Tolkien as influences in the process of my becoming a Pagan, because of their positive attitude to the natural world and the old gods (for example the bit at the end of Prince Caspian, where Aslan releases the river god from the 'chain' imposed by the Bridge of Beruna that was built by the Telmarines, and Bacchus and the Maenads dance through the woods). I was a Christian when I first read the books as a child, but later realised I am a Pagan, partly because of the wonderful magical worlds of Narnia and Middle Earth, partly because of reading Puck of Pook's Hill and Wizard of Earthsea and of course other factors in my life and spiritual development that had nothing to do with books. I also thought that Aslan was a much nicer deity than Jehovah, and therefore couldn't possibly be the same being, even though Lewis implies at the end of Voyage of the Dawn Treader that he is.
Pullman complains that Lewis's books are peddling a version of the Christian message: "It's not the presence of Christian doctrine I object to so much as the absence of Christian virtue," - well, Pullman's books unashamedly (and far more blatantly) peddle an atheist or at least an agnostic viewpoint. The only bits in the Chronicles of Narnia where it becomes a bit obvious that the stories are an allegory for the Christian story are the sacrifice of Aslan on the Stone Table in The Lion, the Witch and the Wardrobe (but then he is a sacrifice in Edmund's stead and not instead of the whole world, and it is the "even deeper Magic from before the dawn of time" that brings about his resurrection), and the bit at the end of Voyage of the Dawn Treader where he appears to the children as a lamb and tells them that they must get to know him better in their own world.
Also Pullman has taken a lot of his ideas about the Garden of Eden myth from Gnostic thought, and has not acknowledged this (though I suppose it's just possible that he came up with it independently). I think he is right, though, in his interpretation of the myth.
"I thought wasn't it a good thing that Eve did, isn't curiosity a valuable quality? Shouldn't she be praised for risking this? It wasn't, after all, that she was after money or gold or anything, she was after knowledge. What could possibly be wrong with that?"
The other allegations that Pullman makes are that the Narnia stories are racist, sexist and mysogynist. Granted, the Calormenes are a fairly obvious parody of the Arabs, but they are not portrayed as all bad (think of Emeth in The Last Battle) and there are attractive aspects of their culture. Also, the Telmarines are just as bad as the Calormenes in many ways, and they are clearly white Europeans (even if they entered Narnia via an island in the South Seas). As for the charges of sexism, when the boys occasionally make a disparaging comment about girls (e.g. in Prince Caspian when Peter says that the trouble with girls is that they can't carry a map in their heads), the girls respond in a fairly spirited manner with an equally biting comment about boys. Another possible example is when they treat the girls in a chivalrous manner (e.g. when Caspian gives Lucy his cabin in Voyage of the Dawn Treader and Eustace complains because his mother is a feminist) - Lewis is clearly on the side of chivalry. But it has to be remembered that before chivalry was invented (by women in the 12th century), men treated women like mere chattels. Chivalry may be old-fashioned, but it is not misogynistic.
The other specific incident that Pullman criticises is from The Last Battle, when Lucy explains that Susan has lost interest in Narnia because she thinks it's all just a silly game that they played when they were kids, and now she's more interested in clothes and make-up. So Susan remains in this world while all the others go to Narnian heaven (from which you can see the heaven of this universe). Pullman claims that "One girl was sent to hell because she was getting interested in clothes and boys." This claim is simply not supported by the text.
So, in denigrating Lewis and Tolkien, secularists have entirely missed the point that the books may express a Christian worldview to a certain extent, but they are also about the mythopoeic worldview and spirituality in general, and children are not so gullible that they will uncritically soak up everything from a writer, but are capable of reading critically (I know, because I remember as a child disagreeing with some of Lewis's comments about things). Also, his portrayal of Jadis (the Witch in The Lion, the Witch and the Wardrobe) did not put me off witches - I just assumed that there were two different kinds of witches, the wicked sort that you find in fairy-tales, and the village wise-women variety that dispense herbs and healing. That said, I think the portrayal of witches in His Dark Materials is absolutely brilliant, and I wish I'd thought of the idea of daemons (which, incidentally, are very similar to the idea of the external soul explored in The Golden Bough by JG Frazer).
Many people read both the Narnia books and His Dark Materials without ever drawing the parallels between the fantasy world and this world. I've seen Christians happily reading Pullman without turning a hair about the portrayal of their God, and atheists happily reading Lewis without noticing the Christian allegory. Maybe it's because these works are about parallel worlds, and not explicitly about this one, even though you can get to the parallel worlds from this world. Tolkien was a keen advocate of the concept of applicability (being able to apply ideas from fiction to life in general rather than to a specific set of circumstances) and he hated allegory (which was one of the reasons he disliked the Narnia books). But both the Narnia series and Pullman's work are applicable and not allegorical.
Whilst I am concerned about Pullman's attacks on Lewis (who is, after all, dead and hence unable to defend himself), I am also concerned about evangelical Christians trying to hijack the Narnia books and use them as a vehicle for the Christian message, and also about them attacking Pullman's work (or for that matter, JK Rowling's work) because they are afraid of it undermining the Christian message. If the Christian message was that great, it wouldn't need protecting or promoting, people would be instinctively drawn to it.
For goodness' sake, everybody just simmer down and realise that literature is literature, children do have critical faculties and are capable of reading between the lines, and these are, at the end of the day, just stories. We may be inspired by the characters in stories, but we read many different stories, and get different world-views from different authors, which enables us to understand that there are many different possible views of the world, and synthesise our own individual world-view from the many different versions available to us.