I don't think morality is something that whimsically changes with time. Instead, I think it took humanity many thousand years to reach the point where the important questions of morality and philosophy could be addressed. Once the biggest questions were tackled, less important questions could be addressed, and so on.
When we were fresh down from the trees and newly able to communicate, we simply didn't have the language or the need to express the concepts or deal with morality. It was eat or be eaten. Later, we started to form cities (large groups living together, that is) and indulge in agriculture (which required cooperation). Only at this time did certain complex moral questions (eg, is it OK to kill my neighbor if I want to divert his water to my fields?) arise. As long as we were fighting the earth for merest survival, no one had the leisure to bother with time-consuming issues of morality.
Finally, though, we achieved a certain level of lifestyle that afforded us time to think. When this first level of moral questions arose, they were addressed by the likes of Mosaic Law and assorted eastern philosophies. The really big questions were addressed and answers proposed. Then, after a few hundred years, some principles were agreed on (at least locally) and the principles trickled down into day to day society.
Once these really big questions had been addressed and the concept of laws and the rule of law more or less adopted by civilization, our lifestyles and wealth increased. This gave us even more free time to debate somewhat lesser issues - say, the human rights of people captured in battle.
This trend has gone on and on, taking us to less and less important issues to the point where we now dither endlessly about silly stuff like school prayer and campaign finance reform.
Through it all, though, it still hasn't been OK to off your neighbor and divert his water to your own crops. The whole idea of morality changing over time is, IMHO, a chimera propounded by people who want to justify either their own actions or the actions of some group they feel sympathy towards. We're not changing, we're just refining to ever more trivial cases.