I liked the film, especially the stunning cinematography, but Amenabar took many liberties with the historical record. Some of them quite major. Here's a good review by an atheist and historian.
http://armariummagnus.blogspot.com/2010/05/hypatia-and-agora-redux.htmlBrief excerpt:
The final major invention by Amenábar which also suits his agenda is the rather fanciful idea that Hypatia was on the brink of not only proving heliocentrism when she was murdered but at establishing Keplerian elliptical planetary orbits into the bargain. The film makes reference to the fact that Aristarchus of Samos had come up with a heliocentric hypothesis in the 300s BC, and mentions a couple of reasons it was regarded as making "no sense at all" (though doesn't mention the primary one - the stellar parallax problem). But it invents a series of scenes depicting Hypatia pressing on with this idea despite these (then) not inconsiderable objections. The whole purpose of these sequences is to make the murder of Hypatia seem like more of a loss to learning at the hands of ignorant fundamentalists. Hypatia was certainly renowned for her learning, but there is actually no evidence she was any great innovator, let alone that she had any interest at all in Aristarchus' long-rejected hypothesis. Once again, it's Amenábar's invented elements that work to support his agenda of simplifying the story into one of "ignorance and fanaticism versus scholarship and inquiry".
The movie also heavily implies that Hypatia was entirely non-religious or even an atheist - something else not found in any of the source material. Confronted with the accusation that she is without any religion ("someone who, admittedly, believes in absolutely nothing") Hypatia replies, rather vaguely, "I believe in philosophy". Later Cyril describes here as "a woman who has declared, in public, her ungodliness". Yet again, Amenábar invents something that has no basis in any of the evidence that suits the sermon his movie is preaching.
Over and over again, elements are added to the story that are not in the source material: the destruction of the library, the stoning of the Jews in the theatre, Cyril condemning Hypatia's teaching because she is a woman, the heliocentric "breakthrough" and Hypatia's supposed irreligiousity. And each of these invented elements serves to emphasise the idea that she was a freethinking innovator who was murdered because her learning threatened fundamentalist bigots. The fact that Amenábar needs to rest this emphasis on things he has made up and mixed into the real story demonstrates how baseless this interpretation is.