As are a majority of people, you were probably raised with a thorough indoctrination in religion of one kind or another. Although you may have grown up, questioned the beliefs you were brought up with and eventually rejected them, that indoctrination is not so easily erased.
Think about other things we teach children as "absolutes". Take for example, lying. We teach children that lying is wrong, that it is BAD to tell a lie, that others will be sad or hurt if they lie. But people DO lie, GOOD people lie, pretty much everyone lies, to varying degrees. Whether for personal gain, self protection or to spare the feelings of someone else, we lie. As an adult, we recognize that as a fact of our being, yet how often, when you omit the whole truth or lie to protect someone's feelings, do you have a moment when you feel guilty for "lying"?
Same principal with religion. You may know intellectually that "God" does not exist and you may understand where the myth began but there are likely to always be moments when your early training pops up. Don't be shocked if, when you hear that your child was in an accident, for an instant a "prayer" for his safety pops into your head. Yes, you will dismiss it because you know a "divine being" is not going to intercede on his behalf but at times, particularly times of stress, what you learned as a child will resurface.