I seem to recall some sympathetic Muslim characters in Pitch Dark.
yeah, i think Pitch Black did a good job making his religion seem serious-but-natural.
I had an interesting conversation with my wife recently after watching a particular episode of "Babylon 5", where Commander Ivanova sits Shiva in memory of her father. To the best of our knowledge, this is nearly the only time in any futuristic Sci-fi where any human character follows any kind of religion that's directly recognizable from our current human practice. The later "Dune" novels also feature a band of travelling Jews, and just like Ivanova, their form of Judaism is entirely recognizable based on modern 21st Century practice.
In addition to the example Jan cited, there was also the recurring character of Brother Theo who was decidedly Christian, Roman Catholic monks in fact, though I don't know their specific order.
i definitely think Babylon 5 did a great job of showing a multitude of views, and showing not just religious nuts, but honest good religious people as well.
However, i'm a little annoyed that religious people seem to have to be in a very formal religion, and we don't really see religious lay people .
And for me , personally, it's not about religion, but a relationship with God. But that would be hard to portray if your universe doesn't actually believe there is a real God.