While some may see this movie as having a not so subtle undertone of 'the greatness of Christianity', I saw it as an interesting exploration of religion itself. The characters in this movie all differ in their religious views, allowing you to identify with them based on your own religious persuasion. There is the fanatic, the believer, the non believer, the good, the bad, the in between etc.
The plot itself helps this journey, as the characters move from one setting to a vastly different one, all the while suffering the same basic experiences. Their initial motivations, in addition to their reactions to these experiences, all differ along the lines of their beliefs, and help either strengthen or weaken those beliefs. This movie shows quite well, that people's attitudes to religion have not changed in hundreds of years. God is still used to explain things we do not understand, and fear and "miracles" are still used to recruit and keep believers.
Human behaviour also has not changed much. Even faced with the 'black death', one of the worst pandemics in human history, people still found reason to divide and fight amongst themselves assigning blame and punishment rather than band together. The way these themes fit in so appropriately with the medieval setting, makes it all the more surprising that they can still be applied in today's world. All in all, a good movie for open minded people because although the film explores these themes, it makes no conclusion. That is left to the audience to determine who was right, who was justified and who was wrong; who was good and who was evil.