Garth Ennis writes many, many different comics. He is also an atheist. He tackles religion a lot in his books. He tackles it fairly hard in his very famous comic series (and rumored to be an upcoming series for HBO) "Preacher." "Preacher" is about a man, Jesse Custer, his former girlfriend, Tulip O'Hare, and an Irishman, Cassidy. Jesse was given this power, referred to as "The Word" which essentially grants him the power to force anyone to do anything. God leaves Heaven after discovering this. He is afraid that Jesse will challenge his authority. Jesse, Tulip, and Cassidy set out to find God and essentially bring him to justice. It has action, romance, adventure, swearing, sex, drugs, S&M, rednecks, guns, weird old people, the mentally handicapped, a fat man, Jesus, and explosions. It's everything the Bible should be, but isn't.
Garth has another book about religion called "True Faith." A young boy develops a disdain for religion. He gets mixed up in the affairs of a man that bombs churches. The two of them get mixed up in a domestic terror plot.
If you don't really want to read something religiously based, he has plenty of other stories ranging from serious tales of the courage and valor of the soldiers in World War II and absurd tales about a superpowered prostitute. He has something for everyone at pretty much any age. I've read dozens of his works and I have not been disappointed by any of them. You might be able to find some of his books in your local bookstore, but you probably stand a better chance of finding them in a comic shop. He's rather famous in the comic book community, so just ask one of the nerds inside where to find some Garth Ennis books. They'll show you and you'll get cool points with them.