It all boils down to the old claim summed up by one of Dostoevskij characters, that “if there is no God, then everything is permitted.” (The Brothers Karamazov)
But loosing one’s faith doesn’t change the individual’s morality. It’s not because we loose our faith that we, all of a sudden, start betraying our friends, robbing or raping, killing or torturing!
It’s just not true that “everything is permitted” because we ourselves don’t permit it. Morality is autonomous, says Kant (Critique of Practical Reason) or it is not morality at all.
The behavior of an individual who doesn’t allow himself to kill just because he’s afraid of divine punishment is not “moral”: it’s just precaution, fear of the divine policeman, selfishness; the behavior of an individual who does good only for his own salvation is not “moral” either.
So, for the faithless ones, there are no longer “divine” commandments, but still there are our moral duties, that are the commandments that we impose upon ourselves.
As French philosopher André Comte-Sponville ( L'Esprit de l'athéisme) says: “Robbing, raping, killing? It wouldn’t be worthy of me – it would be unworthy of my upbringing, of what I am and want to be. Thus I forbid that to myself, and this is what we call “morality”. There’s no need to believe in God for that; it suffices to have faith in our parents and our teachers, in our friends (if we’ve been able to choose them well) and in our conscience.”
I would even say that stats like this one prove that Dostoevskij’s sentence could be paradoxically reversed thus: “If there is a God, then everything is permitted”. In fact, God speaks only and always through men, through their (biased) interpretation, thus every “moral” dictate, even the more questionable, can present itself as being of divine origin, and justify virtually everything (violence and war included).