"The most telling aspect of His Dark Materials ... is that the Reformation never happened in the world of The Golden Compass. Indeed, Pullman's simplistically harsh view of the church and God posit a power-hungry, misanthropic institution out of control, and a detached, domineering God devoid of grace."
The above assessment by historian, Dr Quinn Fox, is also the feeling I have from the book (and film). It definitely is a darker and deeply cynical work; it is certainly an antithesis to Lewis's Narnia. Why would we want to expose children to such an atmosphere? Even more puzzling, how can an authour simply brush away world history in his fantasy tale? Given what the Magestarium represents, his book would have been more fitting for the 15th century than the 20th or 21st.
Liberalism and its secular religions of atheism, agnosticm, and humanism seem largely made up of people who are paranoid of everything--most especially a "highr power". God encourages us to question, but liberals go beyond this to poke and doubt everything and everyone to the point of madness. HIS DARK MATERIALS is simply one on-ramp to that highway of darkness and the ironic thing is that paranoia usually leads to an obsession to control, and that can lead to the very authoritarian tyranny that Pullman's books encourage us to fight.
As an authour I have to think that Pullman missed the boat. His trilogy of books could have gone to a vastly more rewarding and upbeat conclusion. What if the characters got to the end and found that the Magestarium was indeed evil, not because it derived its power from its Authority (aka God), but because it decided to take power from the Authority? What if the ultimate quest of the books had been to free the Authority so that all could benefit from the goodness and light that the Magestarium wanted no part of?