Pavel, my friend, I think it is a pretty big stretch to call it "Stockholm Syndrome". I believe that HH Pope Shenouda III's outreach was sincere (I've seen and read many an account of him visiting Muslims and praying over them in the hospital, for instance; presumably these are moderate and non-sectarian enough to welcome that, so why shouldn't he do it), and every Coptic person I've talked to -- including monks -- has been very proud of their positive interactions with Muslims, such as when they attend Coptic language classes in churches and such. Again, these are the moderate Muslims who obviously don't reject Egypt's pre-Islamic identities.
The trouble is, of course, that not all interactions are peaceful, as not all of the society is moderate. And when that's the case, the blame can hardly be laid at the Coptic side for being too friendly or in any way standing up for the Church's tormentors. Consider the same Pope Shenouda's reaction to Egyptian court rulings which mess with the Church's prerogative on the question of marriage and remarriage:
Or consider the Church's reaction to the slaughter of pilgrims on a bus bound for the monastery of St. Samuel the Confessor:
Just because they don't say anything against Islam directly doesn't mean there is Stockholm syndrome going on. It is just a matter of being a minority in the country and knowing that there are some things that you can convey to your congregation that you probably shouldn't say on TV. That's what makes Fr. Zakaria different. He lives in the West, of course, and takes advantage of that in having his show be as confrontational as Islam usually is to us (and yet still not, as he does not call for violence against them). But that doesn't mean that the rest of the Church has some esteem for Islam as a thing, even if they recognize (rightly) that calling for the repeal of article 2 of the constitution, for instance, would be a losing battle which would extremely unwise to engage in. The congregation into which I was received in New Mexico once got into arguments over the Agape meal because one of the men was mad that another wouldn't teach his young daughters, born here in the USA, that Muslims worship the devil. "Well it's true, isn't it, Abouna? Isn't it true that their god is the devil?" God bless Fr. Marcus, he replied: "Yes, it is true, but you must be careful that in proclaiming this you yourself do not become a devil too." That stopped the argument to everyone's satisfaction and relief.
That's the Church's way when it comes to matters like this, insofar as I've seen it: practical without compromising anything. I would consider Fr. Zakaria's approach problematic only insofar as it is much more openly confrontational, but even in typing that (which I don't actually believe; I like Fr. Zakaria, I'm just trying to see why others might not) I also recognize that there were several centuries after the initial Islamic invasion in which Copts were still confronting Muslims in open armed revolt (e.g., the Bashmurian revolts lasted over a century, c. 720-832), and I've never heard anyone in the Church say a bad word about that period of their history, so this idea of a pacifistic, servile minority is not really sustainable unless you only choose to look at those statements and periods in which the Church was prevented from speaking out or acting out against the second class status of Christians in the country, which is obviously not the case in the modern era, particularly since the Ottoman reforms of the Tanzimat era (1839-1876), which among other things abolished the jizya tax which had led to so many apostasizing in Egypt.
