One of the major concerns with the His Dark Materials trilogy is the perceived anti-religious content. After all, the Church is portrayed as being completely devoid of morals and steeped in absolute evil, and come the end of the trilogy even God Himself is dead. The second ‘fall of Eve’ is something not only necessary to the continuation of the plot, but is actually desirable to the protagonist and those who side with her.
With all of this considered, the Church has every reason to complain, does it not?
With the exception of the fall of Eve, which is described as thus in the text, His Dark Materials is actually none of the above. The important part to take from that is His Dark Materials is not at all anti-religious. It is simply against the concept of organised religion; the rigid structure of rules and commandments that religion has become.
In Lyra’s world, the dominant power is the Magisterium. This organisation is a clear parallel to the Catholic Church of the Medieval Era in our world, or at least a continuation of it. There is no real attempt to disguise this similarity.
At the head of the Magisterium, in the position of God in the Catholic Church, is The Authority. At first we are led to believe that The Authority is the real act: he is God, just with a different name. This is a different universe after all, and there are many name changes elsewhere. This is definitely something that the detractors of the trilogy take, and they run with this understanding and don’t once look back to make sure they are actually correct.
They only read so deeply as to understand that The Authority dies near the conclusion of the third book, which happens quite uneventfully and without the general clamour you might expect with the passing of the Creator of everything that has ever been. That event really was the final straw for most of the detractors, who had been quite content to consider it blasphemous beforehand. Now it was pure and simple heresy, and should be burnt on the spot without any further judgement required.
However, they should have read the book a little better. Why? Well, because The Authority is not God. What is more, the reader is actually told this fairly explicitly.
In the Adamant Tower, the angel Xaphania quite coolly informs Marisa Coulter about the truth of The Authority. He is not the Creator at all, simply the first angel to come into being. The Authority then claimed to have been the Creator of everything that came after him, and all that came before too. By and large, he was believed. Those who did not were subsequently outcast, and became the rebel angels, amongst whose ranks include Xaphania, Balthamos, Baruch, and, supposedly, Lucifer.
As a formerly staunch advocate of the Magisterium, Marisa Coulter is naturally quite perturbed by these allegations, and nothing much is really thought of the matter after this revelation. Perhaps this is why it is so easily missed, because it is so nonchalantly thrown out and then promptly forgotten about. But its meaning is profound.
It means that the entire organisation of the Magisterium is built upon a lie. Their deity is nothing more than a fraud; a mere angel who possesses the God complex to the highest extreme. Even the afterlife is a lie under the rule of The Authority. The Land of the Dead is not the place of paradise as promised by the Magisterium.
So quite clearly, The Authority isn’t the parallel of God after all. He was said to come into being, implying that he was in fact created. Something else created him. And yet this Creator is never once referred to within the text directly. This mysterious figure in the background is the true God of His Dark Materials. And He is embodied by the thing that most opposes the Magisterium and The Authority. That is, Dust.
All of the negative traits of the Magisterium: greed, power, corruption, etc., are opposed by the positive ones associated with Dust. That is, love, free will, and knowledge. These also happen to be the traits that embody the God we know in the Christian religion.
Understand then that the Magisterium sought to destroy Dust. This was then, quite simply, organised religion attempting to destroy the very essence of religion itself. Despite the best efforts of the Magisterium, Dust is eventually saved by Lyra and Will through an act of absolute love.
This is the message that His Dark Materials is trying to convey. It is not trying to say that all religion is wrong and evil. Quite the opposite.
Religion itself is something that should be saved and cherished. It is merely the rigid organisations that try and claim to know God’s Word that should be dealt with mistrust.