Pullman isn't a 'militant atheist' - it's a ridiculous thing to attach to the man, nor is he at the helm of some sinister recruitment campaign to secularism. His books simply (complexly?) put an alternative view that the path to wonder and joy can also be found outside of religion. And it can. Don't we all get exactly that from reading Tolkien, having a walk in the woods or watching kids smile?
One of the 'points' to Lyra is that she is an ''Eve" figure, one of the symbols of the Bible which Pullman finds most interesting as it is Eve who discovers Learning and Knowledge and yet she is thrown out of Paradise for having a mind. Lyra defies Authority in seeking to find out what this Dust business is all about and she too acts like Eve - but in Pullman's case, he has written about what would happen if this 'Eve' did
not get punished. And what happens? Some quite beautiful things, actually
In HDM what happens to people who have had their daemons forcibly severed? They become hollow, and in the case of children, they even die - they clearly need the daemon, it being representative of something within us, either soul or imagination, whichever you like. This is done in an attempt to stop Dust settling on them as they begin to become young adults. The Dust is seen as 'bad', as 'sin', but it turns out not to be like that at all - we don't get told what it is exactly, but we have a good idea that it's something essential to human life, something which separates conscious (self-conscious?) beings from animals. It's also fading from the Universe/s.
Lyra, in defying Authority, and in being brave and learning things, discovers all of this and learns how Story is one of the few things we have - that when we die what is left but our Story.
All of this is incredibly similar to Tolkien's way of thinking, that to attempt to trap and control the imagination and to suppress it is a terrible thing. Lyra discovers the limitless possibilities of other worlds, learns not to tell lies and be true to her own Story and most of all to see Learning as important. This is also what Tolkien tells us, that liars and cheats do not win out, that we must learn for ourselves what is right and wrong (who's there out in the wilds telling Frodo and Sam what to do? Nobody, they must decide for themselves), and to be brave.
I think it's a sad thing if people refuse to read this wonderful book by Pullman purely because a man tells them not to. Terribly sad...
I suppose one of the problems is one it shares with Lord of the Rings - it's hard to tell "what it's about" and people feel they must fix a 'meaning' on it all. After all, in this cost conscious modern society every large effort made must have some kind of 'pay-off', mustn't it? And that's probably why lengthy shaggy dog stories like Tristram Shandy aren't popular these days - all our reading must have some kind of 'purpose' - pur-lease.... Well, meanings are there to be found if you so wish, but it
is just a good story, just like the equally daunting Lord of the Rings.