[Taraz]

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There's always the fact that not all religion came from the Middle East (though I admit these are probaly what shows up the most), and some might not have the "follow us or die" theme.

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What is this in reference to?

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Though I must wonder how much intolerance and violence comes from the religion itself. I mean people will fight over any reason. I suppose there are violent and hateful ideas in a number of religion, but not of their followers necessarily adhere to it. The reason how I can take the Old Testament in the Bible seriously even though I do believe in it, is that the context of the times was harsh with a lot of uncertainty going on and thus the tone of everything sounds really harsh, and God is harsh as well.

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My contention is that not much intolerance and violence comes from religion inherently. However, ideological thinking and in-group/out-group dynamics do. So while religion lets people fall into these traps, many other things do as well. You can make the argument that religion provides no positive benefits and only allows people to fall prey to these negative aspects, but I believe this view is mistaken. As a matter of fact, even if this claim were true, I don't think ostracizing theists would go very far in changing minds.

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But I wonder:
Would the Crusades have happened if there wasn't Christianity or Islam?
Would Al Queda exist without Islam?
I'm quite sure there would still be conflict in the same places just because of people having clashing agendas, although the degree of the conflict might be diffrent.

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I agree. Religious strife has definitely been the cause of some conflicts, but it's hard to parse out how much has to do with religion and how much has to do with culture and ethnicity (especially since religion shapes culture to a large extent).

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Also Taraz:
How has religion gotten more tolerant? Have they gotten more tolerant towards other religions? What about atheists/ nonreligious people? Yes, there is a difference here.

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I think I misspoke when I said religion became more tolerant. I shouldn't have used the word "tolerant" necessarily. Basically religion was moving along with modernity and society. People were accepting the social change that was going on or at worst ignoring the change. There wasn't really an active campaign of conflict. Although the higher institutions (the Catholic Church for example) tried to ignore/dismiss modernity, most people simply lived their lives and didn't really worry about it.

I don't want to claim that there wasn't tension between science and religion, but it wasn't that big of a deal for most people. It had always been there and there was no general crusade to reject rationality.