In many of these societies, theology became a further way of oppressing the people under their rule and a system of thought that sought to get away from this was developed. In Muslim countries this arguably was never developed because the Qur'an stressed never imposing religious belief on the conquered individuals. It is only each person that can come to a decision about what they believe and traditionally Muslim conquerors never imposed Islam on the people of the Christian or Jewish faiths living in the countries that were conquered. Islam rejects secularism as opposed to it's teachings. Logic implies that if God indeed is the supreme master and ruler of the universe and the guide to the lives of humanity then any such separation should surely come from His own rule. By separating society and government from God, there is an implicit act of defiance, of discarding belief, that goes against the most basic tenets of Islam.
Many Muslims do not believe in atheism or in the rule of man. In the eyes of Muslims atheism is the rejection of God and the replacement of God with an idol, the false God of secularism. Secularism is commonly accepted by Muslims as completely contrary to Islam in every respect. It's home is in the West as it was born from the unique set of circumstances and experience particular to Christianity and its spread around the world. In Islam, a religion that by its very definition is a complete surrender of every aspect of an individual's life to the rule of God, secularism has absolutely no place at all.
The Qur'an warns of a concept that is very close to secularism, the worldly life. The wonders of the world that surrounds us, and the very fact that it is in our consciousness and experience can pose a danger as it can distract man from the afterlife, from what is beyond our senses. It is important to understand that the Qur'an does not prevent Muslims from appreciating the wonders of the world around us or from acquiring knowledge. In fact, the Hadith states that man should strive the find knowledge of the ultimate nature of things. The warning in the Qur'an is to not forget that this world is ephemeral and that beyond it and in it is God.
A basic quandary for all Muslims is finding the balance between prosperity in this world while preparing themselves for the Hereafter. The Qur'an denies this dual form of existence and seeks for man to unify his life and the rule of God in every aspect of his life. Secularism states that there can be at once belief in God while at the same time excluding God from the affairs of our worldly life. This is denounced in the Qur'an as unlawful and against the teachings of Islam. According to the Qur'an, man cannot accept two rules, one from God and one made on this world. There is only one God and Islam is the act of submitting completely to God.
The newest generation of Muslim has been gradually moving towards a more secular form of government. As it once arose as a backlash to the excesses of Christian missioners and rulers, it is now again rising in Muslim countries as a backlash against the excesses of extremists and totalitarian governments. Aberrant readings of the Qur'an and Hadith have resulted in societies in which basic human rights have been severely violated repeatedly. Protests in Muslim countries could arguably be attributed to decades of abuse by corrupt governors backed by religious scholars corrupted by tradition and greed in their interpretation of the Qur'an. While the Qur'an is quite explicit in its protections of human rights, the rights of women, and of personal freedoms of all kinds, many extremist governments have used it to violate the human rights of their citizens. Even though the Qur'an explicitly states that Christians and Jews are protected in their freedom of religion, extremists have tried to use the Qur'an to impose Islam on those that are not willing to become believers. If followed correctly, the laws in the Qur'an give rise to a society that guarantees individual freedoms and protects the rights of its citizens while at the same time allowing Muslims to live their religion to the fullest. It is a pity that today's models of Muslim society are ruled by extremists or people with their own agendas rather than by a true reading of the Qur'an.