In the Flamel series, it was made clear that Quetzalcoatl is a Dark Elder. He wants to bring back the Elders from hiding. I don't remember any explanation how he became a Dark Elder, though.
However, Quetzalcoatl mentioned that he was with Aten while Aten was ruling Egypt.
Machiavelli's research on his Master revealed that Aten were considered an enemy of the ancient people of Egypt.
My theory is: Aten and the ancient people of Egypt turned against each other. Whether Aten is truly a tyrant, or the people are just exaggerating is anybody's guess.
Since Quetzalcoatl is loyal to Aten, maybe we can assume that the people of Egypt fought against Quetzalcoatl as well.