I came across a film called The Ledge that supposedly has an explicit atheist as a main character. The film’s website has this press release:

The Ledge is the first film in Hollywood history that puts an atheist into the hero role in a production that features A-list stars. It is written and directed by Matthew Chapman, the great-great-grandson of Charles Dawin, the scientist who discovered evolution, the biggest challenge to religion since Gallileo. The film was nominated for Best US Drama at the 2011 Sundance Film Festival and stars Charlie Hunnam, Sons of Anarchy, Liv Tyler, Lord of the Rings, Tony, Emmy, and Golden Globe nominee, Patrick Wilson, Watchmen, and Oscar nominee Terrence Howard, Crash, Iron Man.

On the rooftop of a city skyscraper, Detective Hollis (Terrence Howard) pleads with Gavin (Charlie Hunnam) not to jump. What he does not know is that Gavin, an atheist, is involved in a deadly feud with Joe (Patrick Wilson), a Christian extremist. Joe’s wife, Shana, (Liv Tyler) is caught in the middle as Joe seeks to test Gavin’s faith or lack of it. Cutting between the present and the past, tension escalates as verbal shots give way to deadly threats in a race against time that neither God nor the police can stop. Along the way, the film provocatively explores the intellectual and emotional conflicts between religion and atheism.

Here’s the trailer.