[WS:] I am not so sure. We commissioned a study of civil society (including unions) in Egypt some 12 years ago, and it did not look that impressive.
Our associates reported pretty much tight government control of these entities, including 'seconding' state employees to work with many of these organizations, which boosted the numbers but also gov control. So unless something dramatically changed in those 12 years - the situation may not be as strong as you suggest. But then again, if someone did a study of civil society in, say, Czechoslovakia in 1979, things did not look very impressive either.
It is quite possible that the military will want to work with civil society orgs to gain legitimacy for the new order, but this is a mixed bag afaik.
Unions and professional orgs used to be the strongest component of the cso, but recently a whole bunch of Islamic charities emerged around the Middle East (I have no information on Egypt though) and these may not be exactly the most left-leaning elements.
Wojtek