Yes. Democracy vs Communism was framed as a holy war by all involved. "Holy" does not imply religion. The Crusades were a power play between East and West Europe, a power play which has it's origins not in religion but in Greek and Roman rivalry for control of the Roman Empire.
Yes. Preying on "witches" are a cultural universal for all mankind, you see it in all of human history regardless of culture, people or religion. And European peoples torturing and burning people who aren't them is an ancient practice--it happened before it was associated with religion. Do you think the Celts burned their enemies because their gods told them to? No, they did it because you burn them and they fear you.
Yes. If you really think that Al Qaeda is about religion, you need to read some history. Islamic terrorism is now, always has been, and always will be a political movement.
The cultures of the Middle East have always engaged in this kind of warfare, regardless of their religion and before religion was a meaningful part of their cultures.