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If God didn't create the universe, where did it come from?

First, let me point out that even if my best answer were "I don't know how the universe was created," that does not imply that "God must have created the universe" is a reasonable explanation. In other words, my inability to offer a reasonable explanation does not mean that devine creation is automatically a reasonable explanation. Devine creation still needs its own justification if we are to take it seriously -- and I know of no reasonable justification. Do you?

Throughout history, man has attributed the things he could not understand to the hand of God or the hands of the gods. But as history unfolds, the ability of later generations to analyse their world constantly improves, man dispells those myths one by one. This historical trend teaches us that that man will continue to find natural explanations for things that he currently attributes to the devine.

The universe itself was once a complete mystery, let alone it's creation. Long ago, the Earth was believed to be fixed and flat.

Sailers used to worry about sailing over the edge!

In Hebrew, there is only one word for both "sky" and "heaven": shamayim. For the writers of the Hebrew Bible, nothing existed beyond what could be seen by the naked eye: the earth under foot, and the sky above containing the clouds, the stars, the sun, the moon... and heaven.

Today, we know that sky "above" is the space that contains our solar system, which is but a spec in our Milky Way galaxy, which is one of the galaxies in our Local Cluster, which is one of the galaxy clusters in our Virgo Supercluster, which shares the universe with our countless Supercluster neighbors. We use our knowledge of quantum physics and relativity to construct and test models of the first seconds of creation. We are still learning about the origin of the universe... but we have come a very long way from the facil "God did it" beliefs of our predicessors.

Doesn't the concept of morality prove that God exists?

I'm not sure why anyone would think morality is evidence of God but I'll take a stab at the question anyway. My guess is that the question presumes that morality is not something that could evolve in humans but only come from God. For some people, the questions may also presume that this same morality is reflected in devine texts (like the Bible for Christians, the Talmud for Jews, the Kora'an for Muslims, etc.). Let me respond to both of these 2 point -- I'll start with the last one first:

Doesn't the moral code of the Bible prove that the Bible is devine?

Various religions claim that their holy scripture teach divine morality. Since the holy scriptures from different religions do not agree, at most one of those religions could be true. Since I am personally most familiar with Judeo-Christian scripture, I'll use the Hebrew Bible for this response.

Logically, if our sense of morality is from God and the moral code reflected in the Hebrew Bible is from the same God, then the moralities should match. Further, people that are not Christians (Atheists, Budhists, Taoists, Jains, etc) should all share the same morality since even though they believe differently, their morality is from the same God. Here are just a few statements from the Hebrew Bible that reflect certain moral values which most people, including Christians and non-Christians would not find moral:

If we feel that slavory and the murder of innocents and witches is immoral, we have to make one of 2 conclusions:

1) Based on our sense of morality, some things in the Hebrew Bible are immoral.

2) Our morality is faulty, therefore the Hebrew Bible's morality may still be impeccable.

However, if you conclude that our sense of morality is faulty, that conclusion has important implications:

1) Our faulty morality is not divine and therefore is not evidence of divine morality.

2) Because our morality is faulty, we are incompetent to judge the morality of the Hebrew Bible and to conclude that it is divine. If we are to believe that the morality in the Hebrew Bible is divine, we must have other reason other than our own moral judgement to believe it.

How could morality have evolved naturally?

We should take a look at what we really mean by morality. A simple definition that may serve for this response is that morality is the "golden rule": "do unto others what you would have other do unto you" (many of the worlds religious scripture includes the golden rule). The golden rule implies that you would not steal, murder, etc, since you don't want to be robbed, murdered, etc.

I think that morality is the result of evolution. There is a common misconception about evolution: that natural selection occurs only for individuals. In fact, evolution occurs for populations as well. This type of evolution is commonly termed "group selection". The development of specialized workers among different species of ants and bees is a good example of group selection. Daughter bees insure that the queen bee reproduces, rather than reproducing themselves. Worker ants feed the entire ant colony rather than keeping all of the food for themselves. Species of ants and bees who developed specialized workers were more successful than species that did not, even though individual workers were not as successful as they queen.

Also at the foundation of morality is empathy. We feel bad about hurting others because we empathize with others: we "feel" their pain. Frans B. M. de Waal says in The Evolution of Empathy:

Humans have evolved altruistic traits (human mothers will die to save their young, just like many other species) as well as the ability to empathize. Also like other species, we have evolved the ability to cooperate with other humans to form civilizations. Finally, like other species, we have evolved a sense of family and other social bonds. These inherited abilities, along with our language abilities and our ability to reason, are the ingredients of human morality. We develop complex rules of conduct and we feel bad (empathize) when we hurt others. We teach these rules to our children who in turn teach them to their children. Over time, the rules are formalized and recorded as law. We can get a sense of how morality changes over time by looking at ancient legal systems (e.g. Code of Hammurabi, Deuteronomy, Rabbinic Law) and comparing them to more modern legal systems (see The Avalon Project at Yale Law School  for a very large collection).