The movie, yes. However, I have read an interview where Pullman essentially said he wanted to do for atheism what C.S. Lewis did for Christianity. Note that I haven't read any of Pullman's books to see if there is any merit to his claims (or how successful he was in this endeavor), but there you have it.From what I heard that Pullman movie bombed in theaters, and the atheistic elements of the books were watered down, but I haven't read or seen either so take what I say with a grain of salt.
Actually, I've been thinking about this off and on today, and I think that there may be another place where atheism is presented in a positive, albeit subtle light - Star Trek. Gene Roddenberry was an atheist (even though he was married in a shinto ceremony - not sure how that works...), and I think he had it in mind that, by the time Star Trek rolled around, most of humanity had outgrown such "silly superstitions" of religion, and hardly anyone even thinks about it any more. The few times religion is presented in the series (to the best of my recollection - I'm sure other more diehard Trekkies will be willing to correct me), it's typically something that other aliens do. There are extremely few references to real-world religions in Star Trek, or indeed, many of the shows that try to follow the same example. There are notable exceptions, of course - Babylon 5 and Battlestar: Galactica come to mind - but for the most part, science fiction in general tends to treat religion as a thing of the past, rather than a current lifestyle.Now, you could argue that Christians also get mocked and treated unfairly in popular culture, and I would agree with you. The difference is there are also many places where Christianity and faith are presented as positives. Look at TV shows like 7th Heaven, Touched by an Angel, etc. There really isn't an equivalent for open atheism, and most open atheists are presented as jerks or pariahs. Now, some of that comes from us being a pretty small minority, and again, it's not about atheists vs. conservative Christians, it's about not fitting the status quo. I'd say moderate to liberal Christians probably fit the status quo pretty darn comfortably, but then that's through my biased lens.