Kohlberg theorized that the development of morality came in stages, and thus, stages could be stifled or stopped, but not skipped.
The first stage is the stage of very young children and is called preconventional. Morality for them is defined as obedience to authority. If a child is obedient to its parents, the child believes that it is demonstrating moral behavior. In a Christian church, young children are told to, and thus expected to, memorize Bible verses, stay quiet, pray when it is appropriate and to pay attention (or at least to be quiet when the child must attend service with his or her parents). The authority figures are adults whom the child has been told (possibly even threatened) to obey. Thus, a child will develop the idea very early on that performing meaningless rites, learning ancient stories and being able to regurgitate them on command are all moral actions because they are doing what their authority figure told them to do. This is why churches push Vacation Bible School so hard. Lazy parents get to drop their kids off at a free babysitter, and churches get to train children that being Christian is moral.
The second stage is called conventional. This is the stage that most professing Christians are stuck at. At this stage, the individual denotes morality with the idea that a person in higher authority must therefore be a very moral person and their word should be trusted. The moral person will follow the authority figure because the authority figure must be trusted to know the difference between right and wrong. This is how the idea of being buddy-buddy with God came to pass, and how the idea of 72 virgins for Mohammedans who blow themselves up came to be. At this stage, unless the authority figure shows themselves to be completely worthless of respect due to a catastrophic moral failure, every word they utter will be completely believed.
The last stage, which most Christians do not fully reach, is called the postconventional stage. At this stage, morality is based on higher principles than just because an authority figure said it. Authority is questioned and scrutinized against other factors weighing on the particular situation. Cause and effect become more important than tradition or dogma. It is at this stage that Atheists emerge. Atheists don't care what Christians or any other religion say is right or wrong until we have considered the facts and the big picture.
This is why Atheists reject the Christian god. Richard Dawkins explains why Atheists reject the Abrahamic god:
The God of the Old Testament is arguably the most unpleasant character in all fiction: jealous and proud of it; a petty, unjust, unforgiving control-freak; a vindictive, bloodthirsty ethnic cleanser; a misogynistic, homophobic, racist, infanticidal, genocidal, filicidal, pestilential, megalomaniacal, sadomasochistic, capriciously malevolent bully.