A really interesting book on this subject is Christopher Hill's "The World Turned Upside Down: Radical Ideas in the English Revolution". Hill was a Marxist of the mid-20th century, so I assume he was also an atheist although I'm not 100% sure.
He talks about how the entire social order of feudal England was predicated on the belief that the King was God's agent on earth, and divinely selected for his position. Around this concept, a repressive system develops, kept in place by religious elites who "interpret" the (Latin) bible and thus back up the King's claim in exchange for land and wealth.
So, religion here is the enemy: an oppressive intrument, right? No, religion is a concept that is used by the powerful to legitimate their own rule. King Charles doesn't hang onto power because he believes god wants him to. He says that god wants him to, in order to hang onto power. Why isn't this facade seen through? Because the only people that were, at the time, educated enough to realise that this "divine right" has no support in the bible are the priests, who are bonded to the king through power and money and land.
The biggest ballsup the ruling powers made was allowing the Bible to be translated into understandable English, so that ordinary people were able to interpret it for themselves. People start to realise that subservience is not the word of Jesus. As such, ALL of the unrest and questioning of that period that led to the English Revolution and the beginnings of parliamentary democracy were not based on seeing through religion: they were actually based on a
more democratic and more authentic interpretation of the bible itself.
Gerrard Winstanley, IMO one of British history's greatest heroes, (
http://en.wikipedia.org/wiki/Gerrard_Winstanley) couched everything he said and did politically in religious terms. He is an inspiration to atheists, because he was one of the very first people to question the literal truth of the bible, arguing that it should be viewed as metaphor. But, this doesn't change the fact that he saw the oppressive rule of Charles I as anti-Christian. In fact, many people of that period began to view the priesthood as a series of anti-christs.
The point of all of this is that in a great many cases religion is not the "cause" of a great number of things that it is supposed to be the cause of. The "cause" of the oppressive rule of the King was lust for power, not religion. Religion was simply a means of rationalising it. The rebellion against the King was not religious; it was a result of many, many social factors. But religion was again used as a tool to legitimate that rebellion.
What I'm trying to say is there are many things which are far more fundamental than religion in determining what happens in the world. Even the example of the Danishs cartoons. Dunno about the rest of the world, but in the UK there is a very strong perception amongst some sections of the Muslim community that they are marginalised in British society. Whether you agree that that's true or not is irrelevant. What matters is that this perception was far more fundamental to those protests. The fact that someone had drawn a cartoon was a legitimating tool rather than the real issue.
Eeesh long post I'd better stop now and get some work done.