They do so despite the foundation their core beliefs rests upon.
How? And what difference does it make, if they're doing it? Doesn't seem like making sense of origins is hurting their ability to act in this way. Now to your questions.
why does anything at all exist?
Don't know.
How does the universe begin, if you think it began?
All evidence points to time beginning at the big bang. Before that, don't know. In either case, makes no difference to my life every day.
we can trace the universe back to that first cause, but no further. How does that make sense?
Don't know. Again, immaterial to my life.
Did the universe create itself, and how, why?
Don't know.
How did conscious living beings come from non-conscious, nonliving matter?
Don't know.
What knowledge are you speaking of?
How the universe started.
You do not rape because you think raping is wrong. In an indifferent universe what does it matter and why are you making it matter?
I don't have the compulsion to rape anyone. Weird, huh? I also know a lot of non-rapists, and not just atheists. Hindus, Christians of many stripes...I don't want to speak for anyone else, but I doubt many of them would say "God said not to do it so I don't do it." Especially considering god never says in the bile NOT to do it, and in spots seems to condone doing it, provided it's not a hebrew.
In an indifferent universe what is the standard for morality?
There is no standard and there never has been. How do I know? Morality shifts between societies both contemporaneous and in different times, At one time it was moral to beat your wife, and now it isn't.
Whose subjective opinion?
It's not one person. It's society. The one you live in determines it.
Why should I believe it?
Well you don't want to go to jail, right?
You are being inconsistent from your starting point (without God). Why should rape matter in an amoral universe? It is just one member of a species securing their offspring. Ultimately it does not.
You know, now that you've mentionedit like five hundred times, I've decided you make a good point. It DOESN'T matter I guess. Looks like I've got a new plan for my weekend!!! LOOK OUT LADIES! Come on man.
Why are you making meaning matter and seeking meaning if you start with a random chance happenstance universe?
Because I care about my fellow people. Apparently you do it because if you don't you'll be punished forever? if that condition were removed, would you be out raping?
What difference does it ultimately make?
I'm not causing anyone else any harm, that seems pretty good, particularly if I'd rather not have harm done to me. Maybe I don't get the modifier "ultimately" here, maybe you mean something else?
How do you explain justice in a universe devoid of God?
I don't understand why I need to 'explain' justice, I mean do you think it popped into existence with the big bang? Does somehow having the origin of theuniverse knowledge that you have, and I don't, mean you understand justice better? It's sort of a different word for fairness, I guess, but there's also the concept of remediation and punishment in there. Justice is pretty complicated, but it's a human construct (fairness, the simpler version, is not a human construct, animals display a keen understanding of this behavior). Now that I mention it, hyenas understand punishment and rules and morality, too. If a hyena pup steals food before it's his turn to eat, he's punished by being tormented and bitten and outcast even temporarily. That teaches other hyena pups not to do it. They even understand forgiveness, because they've been known to let he pups back into the pack after a time.
All questions answered.