Why do secular champions of modernity feel the need to fabricate false histories in order to depict Christianity as especially brutal, intolerant or anti-intellectual? You would think that in the history of Christendom there are plenty of legitimately objectionable occurences to decry without making stuff up. A few months ago David B. Hart wrote a brilliant piece in response to the release of Alejandro Amenábar's Rachel-Weisz-starring film Agora in which Christians are depicted as particularly intolerant, brute savages who were opposed to the advancements of Greek science on philosophical grounds, and for that reason murdered the secular, Greek scientist-philosopher Hypatia and destroyed the Great Library of Alexandria. Hart goes on to point out that this 'history' is an utterly fabricated narrative with virtually no foundation in any evidence whatsoever. And, in fact, the evidence that there is paints an entirely different picture altogether.
The key points being that while Christians did in fact murder Hypatia, it wasn't because of her intellectual, scientific pursuits (which were also engaged in by Christians and which Christians did not object to), but because of her role in a political dispute in the city. Of course this doesn't make the act any less heinous or objectionable, but it does refute the narrative context of the supposed reasons for their actions. That is to say; it wasn't their Christianity (clearly), or their hatred of secular science that drove these people to such lengths, but rather specific local, political conflicts of the sort that have occured since the beginning of time, and have been engaged in by people of all faiths and those of no faith. Anyways, Hart's piece describes all of this much more fully and ably, so read that.
Of course it seems Amenábar's film specifically is likely the result of inertia; a facile acceptance of poor history. The interesting, broader theme is the stake that the champions of modernity, of the rationalism of the Enlightenment, have in pitting the 'light' of secular science, knowledge and progress against the 'darkness' of intolerant, ignorant and violent 'faith'. That is, how this narrative ever was introduced and widely accepted uncritically to begin with. Especially by focusing on an era of history where such an opposition was completely unknown. Where pagans, Jews and Christians did science and philosophy side by side. It's an anachronism based on the decidedly modern 'conflict' between the two--though that too is often largely exaggerated or fabricated.