Egypt just may be undergoing a similar process that Iran underwent back in 2010. Iran had protests after an election that was seen as being rigged. The end result was those who were brave enough to stand up and expose themselves were then identified. Over the course of the next few weeks, these people were dealt with. There are lots of ways of dealing with people without resorting to actual elimination, although I am certain that torture and murder were used frequently. However, Iran is different from Egypt.
Egypt was controlled by England for generations. Although the Islamic influence is still ever present, the ideas of a different economic and legal system were established long enough to make some roots. We are seeing this today with the large protests against the government that had been recently elected. The current leadership of Egypt is largely influenced by Islamic ideology and law. The moves being protested against are logical but enough of the population has accepted a different way of rule that we are seeing larger protest than what was witnessed in Iran. What I worry about is a similar reaction by the government. Although Egypt appears to have a larger population that is in conflict with the government, the response will most likely be similar. Identification of those who are the most visible and most exposed. I would expect the initial moves by the Egyptian government to be fairly quiet. Once people begin to shut up, (Threatening families is a good way to do this) it is easier to be open with the moves that follow. People disappearing tends to get others thinking about their own best interests. Islam is good at forcing submission and the influence has not been eliminated altogether, by any stretch.
It remains to be seen what will result in Egypt, but the pattern that I see throughout the Middle East today is victory by Islamic forces and influence. I expect the same in Egypt although it may take longer than in some of the other countries.