I don't think he's saying that learning to program in C caused him to become an atheist. I think that he's saying that learning to program led to an outlook on life that caused him to question his previous beliefs (and then, eventually, to become an atheist).

The difference between programming (and math) and just about everything else that he's probably experienced at this point in his academic career is that when he writes a program, he can test it himself; he doesn't have to ask a professor to verify that it works or look up the answer in a book. That's different from humanities subjects and even most science classes, and it probably led him to realize that he can figure things out for himself and to start questioning things that he'd previously taken for granted.