The first time I heard the question, "where do atheists think morals come if they don't believe in God?" I was baffled. Despite being raised Catholic and associating particular moral codes with particular religions - with gods telling their followers what is the best way to behave and have a meaningful life - I never associated the existence of morality in general with the existence of religion. I never thought people couldn't or wouldn't come up with a moral code on their own (after all, society existed and functioned before God gave Moses the 10 Commandments, and all societies have some sort of ethical guidelines no matter who or what they believe in).
Now that I have a better understanding of what the question is essentially asking - "Why do atheists think it's wrong to hurt others if they don't believe there's a God to punish them for doing so?" - I feel I can answer this question fairly, and it's directly connected to why I left religion in the first place.
The simple answer for me is "reasoning": I don't like to be harmed, unfairly criticized, treated poorly; I care about my relationships (however I define them); I think my interests, thoughts, and inner experiences are valuable. I see absolutely no reason to think anyone else in the world feels differently about themselves, their feelings, their experiences, their relationships, etc. And I can't assign a relative value to my experiences compared to everyone else because I can't experience someone else's life to compare. Therefore, I think we're all equal, and can't think I or anyone else has a right to hurt another (I suppose I might be defining "harm" as "dening the legitimacy of their own experience." I'll tentatively go with that definition until I think more about it).
Essentially, I take a rationalized approach to The Gold Rule* and equality, and combine in with the evolutionary reality that humans survive best in a society (meaning we work together and need to find a functional way to do that).
This all came after I left religion, though. Initially, I simply felt that for me to stay a Christian, I had to believe my inner experience of God was more "correct" than my non-Christian friends' experiences of God or whatever else they believed (otherwise, why wouldn't I be their religion instead?), and I personally didn't feel I could take that position while still fully respecting the legitimacy of their inner self. Leaving religion allowed me to fully participate in equality by acknowledging that what makes us different may not be what we feel, but simply how we interpret our feelings.
*Just because I don't believe in a particular religion or don't see their teachings as the literal word of God doesn't mean I don't think they can have valuable philosphical insights.
