I'm sure there were many atheist, agnostics and otherwise irreligious people ruling during these times. But keep in mind that religion was more that a conscious choice: I'm not saying that people were forced with pikes to go to church (well, in some places...) but it was seen as an integral part of society, the glue that kept many communities together, and a ritual essential for power. I have no doubt that many were either truly devout or outright atheist as many people today, or many things on the middle, but they kept their personal thoughts behind doors and went to church as a part of the social contract, belief aside. I imagine that was the case with most of society: many peasants and bourgeoise were devout, but having a good reputation with the Church earned many benefits for those who weren't.
Also, as one poster said, atheism was very unpopular not only for "heresy" but because the evidence for God's existance was 'clear' to everyone in those times. The Church held most of the knowledge and philosophy from the time, and everything pointed to God. Atheism was viewed more as nihilism or foolishness rather than a conscious choice.