Well, right now the government is essentially run by the Muslim Brotherhood....or I shouldn't say it's run by the Muslim Brotherhood, but the president is from the Muslim Brotherhood and the country's largest political party is the Freedom and Justice Party, a party that does have a very small number of Christian members but is essentially a Muslim Brotherhood political party.
I think that has to be the main concern, that you have a governing party that is Islamic in colouration. As well, it's likely that in the parliamentary elections, when they are held, the Brotherhood party will probably do well, and the next largest party may also be Islamist, of Salafi bent. The tension between Salafis and Christians is much stronger than even that between Christians and the Brotherhood. There is no getting around the fact that Christians are a minority, and that, in a democratic process, minorities don't necessarily do very well.
I think one of the things that would serve Christian interests best would be to insist that Egyptian state institutions—not necessarily those of the presidency and the Parliament, which are probably going to reflect the majority, but Egyptian state institutions, including things like the military, the security apparatus, the judiciary, and so on—be constructed as much as possible on a non-sectarian basis, so that non-discrimination, both on a formal but especially on an informal level, would be a strong principle enshrined in the construction of various state bureaucracies. That would ensure a Christian presence throughout all Egyptian institutions.
As it is right now, my sense of Egypt is that informal discrimination is a very serious issue. Formal discrimination, that is to say, areas that are actually legally barred to non-Muslims, is much less of a problem. The issue will be in a sense enforcing that law, and getting state institutions to take it seriously.