
Hey Godma thanks for the comments I will give a brief response to some of the things you raised.
You write:
"1. There are good evolutionary advantages for people to have an innate moral instinct, albeit a simplistic one (something like "try to be nice to your fellow humans")."
Based upon an evolutionary assumption sure, there may be "advantages" (defining that gets sticky as I will show) to a sort of pragmatic moral code. This however does not equal those actions being inherently wrong, we just define them as such for pragmatic reasons. So rape isn't really wrong but we just categorize it as such because it's effects are undesirable.
Also I think a case could be made that many practices we deem "wrong" in themselves certainly could have evolutionary "advantages". Take random indiscriminate open copulation, like animals practice. We would find it rather immoral if when we walked down the street we saw numerous couples engaging in procreative activities in public in front of young children. Or even rape for that matter could be seen as advantageous and as such "moral" on a strict evolutionary sense.
"Over the long course of evolution, individuals with a genetic predisposition toward being generally nice to their family and tribe-mates out-reproduced individuals who did not have that predisposition. The instinct we have inherited from this is still present. It's not fool-proof, of course, but it can go a long way."
So "nicety" (whatever that is) is genetic? What part of the genome contains this "nice" gene? Can you weigh nice genes? Can you pour niceness into a glass?
Given this strict materialist view of things I wonder how you can say anything is "wrong" at all. I mean people are just acting on how their chemical make up determines them to act. How can you say it is wrong to fail to posses an adequate amount of "nice" genes"? Given such a view I just wonder how we can make any moral judgments on people or call anybody "criminals" because they are simply acting upon their biological makeup.
"2. Human cultures have further promoted habits of moral behavior in their members, through morality stories (including religious stories), social pressures, and rule of law with punishment for transgressors. Over time, the moral sense of a culture does gradually shift due to changing conditions, however (e.g. times of bounty/famine, technological growth, etc.)"
Well, Nietzsche would say these stories were just made up by the weak to control the natural barbaric instincts of the strong. We need to adopt a master morality and reject all of these stories and let "do what thou wilt" be our moral guide. In essence these are all facades and control devices, there isn't any REAL right and wrong, just pragmatic weapons to control people with. Do you live in that world? The world where there is no real right and wrong, where right and wrong are just conventions made to control people?
Or do you live in a world where the rapist REALLY did do something wrong? If you live here I would submit that as an unbeliever you are simply borrowing from my Christian worldview. Indeed this borrowing from the Christian worldview becomes apparent as you will soon invoke the "golden rule" as a moral standard.
"3. Basically, as a culture, we should treat certain behaviors as "good" and others as "bad", for the simple reason that it is beneficial to the culture to do so (in that it helps the culture persist and prosper)."
Why? Why is that what we should do? Why should we care about the culture as a whole? Why should any of that concern me? Why should I based upon YOUR worldview give a rip about anybody else, nevertheless a whole culture of others?
Again your assessment masks that "good" and "bad" are conventions. We just pragmatically employ this "moral language" to control people. The actions themselves aren't actually wrong, we just label them as such arbitrarily.
"For example, I think we could mostly agree that the golden rule is an excellent basis for morality that can continue to endure through time and even be treated as an absolute, with no need to justify it based on the belief in deities. We can justify it based on the fact that it helps us minimize suffering (which is conducive to a peaceful society)."
Why yes I think the golden rule is wonderful...based upon a Christian worldview. But see you have no right to borrow this concept. Once you take the golden rule and divorce it from the authoritative objective word of God incarnate (Christ) then it is just another arbitrary convention made by men that I see no reason to abide by.
So based on YOUR worldview why is the golden rule a good standard to live by? Why should I care about other sacks of chemicals and how they may "feel" about certain actions? Why?
You have simply taken some of the leftovers from the Christian worldview in appealing to this. I submit that this is because you are made in the image of God and that although you deny this God you really do know Him.
"So, my answer to the question, as an atheist, is that it is wrong to fly planes into buildings because it is wrong to cause needless suffering."

Also we need to remember that jihadists and rapists are just acting on their chemical makeup. They are just doing what nature has chemically determined them to do. I would also ask this: Is there such a thing as "needed suffering"? Well then it seems like it would be a matter of subjective perspective to make a distinction between what is needless and needed. I think the Jihadists would say blowing the WTC up was needed suffering. Who's right you or them?
You try to answer my above question saying:
"And needless suffering is bad because it is harmful to a stable and peaceful society. ...And that is something we should try to maintain because it is in our own self-interest in the long run."
Again, who cares! "Self interest" that sounds like a bunch of junk considering that I got about 80 years to whoop it up and then annihilation, why in the world should I give a rip about the "good" (whatever that means) of society or humanity?
You next add onto why "needless suffering" is bad writing:
"I also think it's bad because I have a sense of compassion. Seems obvious, but I thought I should add it just in case."
So because you have these feelings that action X is bad that = moral obligation? What about the sacks of chemicals (people) walking around who don't share those feelings? Like, oh, Charles Manson. So what makes him the bad guy and you the good guy because you when you heard a women being raped in the alley called 911 and went out with a baseball bat to get the attacker off her, whereas on the other hand Mr.Manson pulled up a chair at his apartment window and opened a bag of Doritos and watched the show? Why is he "bad" and you "good" based on your worldview? Are not both paths equally valid?
After all he doesn't have the chemical make up that induces this thing you call compassion, can you really fault him for that?
So again this just raises the question as to WHY I should (based upon an Atheist Materialist worldview) care if another sack of chemicals and nerve endings is experiencing pain?
Now as a Christian I can answer all of those questions. We should care about other human beings because they are not just sacks of chemicals they are creatures made in the image of God, and as such they have dignity and worth. There is no higher value you can place on human life then to acknowledge that we are made in God's image.
Furthermore right and wrong are not mere pragmatic categories invented to make society "work". Ethics and morality reflect the character of God, and thus is implanted in the nature of man made in the image of God (This explains your feeling of compassion for others, those feelings are valid in a Christian worldview). Thus, because they are based upon God, the creator of man and transcendent over man, these standards are objective and universal and as unchanging as God is unchanging.
Furthermore God has revealed His nature and Character not exhaustively but truly in His revealed word the Bible. Thus I have a standard that says why rape is wrong, it is a crime against the person who has worth (being made in God's image) and against God who made that person and has stated that such treatment of others is wrong.
Let me end by saying that you probably are a fairly moral fellow. You would probably say that it is "wrong" to steal for fun or hit people in the face in to see how they react. However, I would say that based upon your worldview you have no reason to think this way. All you have given is pragmatic benefits to having a sort of moral code in a society, that doesn't make these actions wrong, that just means we act as though they are.
I would lastly say that you do know these behaviours are wrong, this is because you are made in the image of God and you live in the world God made. You don't live in Materialist Atheist land where morality is just a convention, you don't live in a world where you see people as just sacks of chemicals and water. You live in a world made by God and you bear his image, yet you in suppressing the truth of God can only offer pragmatic morality to explain what is really there.