In short, the answer is, 'No'.
The Golden Compass is the movie adaptation of a book by British author Philip Pullman. UK title: Northern Lights. US title: The Golden Compass. The book is the first part of the trilogy known as His Dark Materials. That line is taken from the John Milton poem, Paradise Lost.
The books and the movie carry a message to which all free-thinkers will relate: never stop questioning those in authority.
On the other hand, the trilogy is merciless in its attacks on those who seek to control people's thoughts and beliefs. The government portrayed in the book -- the Magisterium -- is deeply corrupt, and seeks to restrict knowledge from the masses, while simultaneously using such 'forbidden' knowledge to increase its own power and further control the population.
Much of the criticism of the book derives from the obvious parallels between the imaginary Magisterium and the real Catholic Church -- especially some policies and practices adopted by the Catholic Church in previous centuries.
The movie significantly downplays the parallels between the fictional Magisterium and the real-world Church.
Some say the books seek to spread atheism by the back door. This claim is easy to dismiss. There is much discussion in the books of "the Authority", which is clearly meant to equate to God. At the end of the final book The Authority's regent is killed. If the character of God's Regent is present in the book, then the book demands a God.
As with Paradise Lost, there is an almighty battle between the free-thinkers and their oppressive rulers. As with Paradise Lost, true love ultimately conquers all and a new Adam and Eve can take humanity forward, freed from the tyranny of those who would control their every thought and deed.
Commentary: many people have written to say something along the lines of "Okay, so what do you say about Pullman's repeated statements about the books being about killing God, and a deliberate attempt to undermine Christianity?"
I say, fair point. Yes, Pullman is an aggressive atheist and is on record as saying he wants to bring down the church and all kinds of stuff like that. To be honest, I don't really know why his books have avoided the kind of flak attracted by Rowling and her boy-wizard. If I were a Christian apologist, I would be much more threatened by Pullman than Rowling. He's a better writer and quite open about his anti-religion agenda. Rowling on the other hand is writing ripping yarns gently seasoned with a little supernatural spice.
Having said that, first, a movie is a completely different medium from a book and this movie adaptation re-tells the story with different emphasis. Second, I don't think the first book in Pullman's trilogy is especially anti-religion. The polemic increases with each installment. I think that aspect of the work is more than adequately covered in the writeups under His Dark Materials. My writeup was an attempt at a short, easy-to-read piece on, specifically The Golden Compass. In the UK (where I live) that's a movie in which the anti-religion agenda has been masked and massaged out of the story. In the US, of course, it is the title of the book, but I already said the true evil of the Magisterium and its similarities to the Catholic Church do not come out until later in the trilogy.
Referring to the movie, I saw it with a group of people -- teenagers with Aspergers and their parents -- few of whom had read the books. About half of them, AspieMum included, are Catholics. Not one of them saw anything in the movie to get offended about. I had to spell it out to them that the books are seriously anti-Catholic, but they shrugged it off as if it were nothing. In the end, I stand by my comments that the recently-released movie titled The Golden Compass is not anti-religious in any way.
Going on from there, as ascorbic rightly points out, the latter two books, especially the third are just breath-takingly anti-religious and specifically anti-Catholic. It remains to be seen whether New Line has the balls to film them. This movie seems to be reasonably successful with the anti-religious themes excised. It will take a clever director to remove those themes from the latter two books and still end up with something that can be recognised as Pullman's work.