Strategy Page has an article about the history of the Copts in Egypt after the Muslim take over:
An ugly and ancient aspect of Islamic culture recently triggered violent demonstrations throughout the world. The cause was a low-budget film (“The Innocence of Moslems”) made by an Egyptian-American Coptic Christian. A minority of Moslems have always been particularly sensitive about their religion and how it should be practiced. These conservatives have gone by many names over the centuries. The most common tags these days are Salafists and Wahhabis. These fanatic minorities have exercised an influence on Islamic culture far larger than their numbers (usually less than 10-20 percent) would suggest.
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This brings us back to “The Innocence of Moslems” and why it was created by an Egyptian Christian who had fled his homeland. He’s one of many, actually. Some 1,500 years ago most Egyptians were Christians, nearly all of them belonging to the local Coptic sects. Then the Moslems invaded in the 7th century and used threats and financial incentives to encourage conversion to Islam. After three centuries of this, Moslems were the majority. Ever since, Egyptian Moslems have sought, often with violence, to convert the remaining Egyptian Christians (currently about ten percent of the population). Some converted, but increasingly over the last century, Copts have simply fled the country. Those who left had bitter, and ancient, memories of Moslem persecution. That apparently led to making the “The Innocence of Moslems” (allegedly financed by Copts in Egypt).
In response the Egyptian government issued arrest warrants for seven Copts (including the man believed behind the film) and an American clergyman noted for his anti-Moslem attitudes. All eight are accused of having something to do with the film. This is a largely symbolic gesture, as all those being sought by the police are outside the country. Copts living outside Egypt frequently say unkind things about Egypt and Islam, but these comments are usually ignored inside Egypt. Meanwhile, a senior Pakistani government official has offered $100,000 of his own money for whoever kills the Egyptian-American man responsible for the film.
Islamic terrorism often gets explained away as being a reaction to Western imperialism, or colonialism or simply cultural differences. No one, especially in the Islamic world, wants to admit that the cause of it all is religious fanatics who would rather appear righteous than be righteous.