The key points in western history to be considered are the Thirty Years' War and the Peace of Westphalia. This conflict and the resulting peace are probably the defining events in what has turned into the European and American relationship between religion and the state as well as setting the basis for the modern nation state.
The war ravaged Europe for three decades over the ability of rulers to choose for their kingdom to be Catholic, Lutheran or Calvinist. The war involved every major and minor state in Europe as well as interventions by the Ottoman Empire in the Balkans. In those thirty years the population of German states were decreased by 25-30%, with some provinces loosing almost as much as 75% of their population.
All of that fighting, and bloodshed, disease and suffering ended in 1648 with the Peace of Westphalia which ultimately reaffirmed the 1555 treaty of Augsburg, which allowed sovereigns to choose the religion of their state and allow religious minorities to practice their faith without oppression. The peace is a peace of exhaustion. An admittance that no amount of bloodshed will make a person believe as you do, that perhaps it was just best to let people be and let God sort it out.
Most people will never think of the war or the peace when speaking of religious freedom and freedom of speech. But the American First Amendment has the underlying intent of the treaty baked in to it. Freedom to choose your religion and freedom to speak your mind. Most importantly the First Amendment extended that freedom to the individual level. That no man may call another man heretic with the force of law in his voice, is one of the most beautiful things about the American experience.
But that is the American experience which is an extension of another European idea and experience. The idea is so inherent to western society, that we forget that it is not a universal value. The Islamic world was not a party to the treaty. The treaty and its ideas are not part of their heritage.
Perhaps collectively they will get there, many parts of the Islamic world already are. Unfortunately at the same time Islamic fundamentalism is growing in some places as people strive to return to a "pure" Islam that created a caliphate st reaching from Spain to Pakistan. The conflicts between Sunni and Shia burn and fester as they have for a very long time.
All of which is bound and rolled in an Arab Spring which seeks to bring freedom from oppression and freedom of speech and association, but also allows them to express their objectionable views, and associate in ways that allow for violence to blossom where previously only repression grew.
None of this excuses violence and murder. None of this should preclude rational assessment that the actions of individuals do not represent the values of a country and culture as diverse as the United States. None of this excuses the perversion and sublimation of religious ideas to derail and influence a political process.
Democracy is hard, democracy is messy, countries are more likely to suffer from internal strife and external conflict during a transition to democracy then any other time.
But we won't make it any better by presupposing ideas from our history on to other cultures and expecting them to become a part of the fabric of a society based on our declaration alone.
Hopefully we can come to agreement on all of this sooner rather than later.