One of the main arguments used to forward the idea that religion should be separated from government is the protection of the freedom of religion for minority religious populations in Egypt. Among them, Coptic Christians, Shia and Sufis as well as the accommodation of the many schools of jurisprudence of Islam. A diverse civil society must be able to protect the rights of all citizens.
This is only one argument and not even the first argument for the issue of division of religion and government.
Many believe that the call to separate religion from the government is only a call to reduce the role of Islam in Egypt and the Islamic identity of the Egyptian people. This is a fear that is unfounded. The majority of citizens in Egypt are Muslim. The strength of the faith and the long relationship of the majority of the people with their Islamic heritage remains unchanged, regardless of the governments that have existed. It will remain unchanged in a society where freedom of religion is protected and the people may practice their faith as they see fit.
This fear is not surprising when a people have been living under an oppressive regime that used government power and money to control the mosque, the selection of Imams and to influence the message. If someone belonged to a religious group or made public religious sentiments that the government found threatening, the group could be attacked and the people put in prison for a very long time, often times tortured and killed.
The Grand Sheikh of Al-Azhar recently announced that he would give back his salary provided by the government because corruption has spread within the institution. Other leaders staged a protest against the corruption born of government interference, payment of bonuses and other devices used to extort responses and control the Ulema.
By these acts the Mubarek regime wished to control the conscience of the people, preventing them from voicing their concerns about the government and the leaders. Acts that are all too familiar in oppressive nations.
What is surprising is that people who have experienced this repression and point to this corruption are so willing to consider the continuation of this same construction of religion and government. All with the apparent belief that this time it will be different.