The Coptic Orthodox's Church's decision to discourage people from participating in protests
may surprise some, but is entirely consistent with that body's focus on the preservation of its religious mission in a nation accustomed to dictatorship. Al-Azhar, the most prestigious source of authority in Sunni Islam, has at its top levels become a branch of the Mubarak regime. The current Coptic Pope, Shenouda III, was briefly deposed by a decree of President Anwar Sadat
for taking too strong a stance against his government, and only restored by Husni Mubarak a few years later. Given that churches see their mission as transcending politics, it is unsurprising that they have taken such an accommodationist line to preserve their ability to serve that mission. Fears of what might happen after Mubarak are also a factor.
Despite this, however, many Copts are on the streets protesting
UPDATE: From Ian Lee
: "A man made a point of asking me to distinguish who was from what religion in the group, I couldn't. That was his point."