Almost every work of fiction, especially genre fare, presents atheist/skeptics in a negative light. If you think about it, it serves a particular function in most fictive works. First we establish “the Other” has come, the bad thing that we are to fear. The atheist/skeptic comes forth to declare that there are no such things as ghost-vampires-zombies-UFO‘s-slashers-pod people, etc, etc. This first echoes our own doubts about such things, and provides a pause in the proceedings where the Other can work his mischief, whilst the people waste their time living their lives, oblivious to the danger that awaits them.
That they are ultimately proven wrong brings a sense of happiness to the audience, as that they are already aware that the Other is present (for if it wasn’t, what would be the point of the story to begin with?) the audience loves to see the smug smart guy die, as they usually do at this point of the story, just as he comes to grip with the Thing that he could not believe in.
Think about it. Wouldn’t the movies be boring if they were right? “The person was killed by a vampire!”, “Non sense! Vampires don’t exist.”, “Oh, right. Oh wait, there’s the killer over there, and he was killed with only one bullet. Imagine that.” The End.
Frankly, I think it would be shorter if we just listed those movies/TV shows that showed atheist/skeptics in a positive light, or at least those shows that let them be right, which would basically be “House” and “Scooby Doo.”