One thing that didn't really make it into the story and that I find interesting is the way these sectarian tensions are tinged and perhaps exacerbated by global trends. The war on terror, the occupation of Iraq, make Muslims feel their religions is under attack; while the fact that some Christians are pro-American gives weight to theories that they are a "fifth column." Meanwhile, the Coptic community watches satellite TV shows and goes to web sites from outside Egypt that are very negative about Islam; they have contacts with expatriate and US evangelical groups, who make a habit of demonizing Islam, to help them put pressure on the Egyptian governments for greater rights. But when an American group talks about Coptic rights, most Egyptians view it as a conspiracy, foreign meddling, and again, a disturbing sign of disloyalty on the part of Copts. It's a big complicated vicious circle.
Meanwhile, you have a generation of young Copts who are increasingly militant about their religion, and tired of feeling like second class citizens. They tattoo the cross on their hand and they put out magazines with names like "The Theban Legion"--a reference to a Christian legion (of Egyptian Copts) that was martyred around 300 AD by the Emperoro Maximinian for refusing to recounce their faith.
I've always found that, despite the fact that Copts do suffer from discrimination, the Coptic church provides poor leadership on these issues, focusing on threats to increase its own influence. We talked to a priest in Alex who, the day after the attacks, told his congregations: "Don't be afraid. If they kill us, we will all go to heaven." Giving people a martyr complex doesn't help them.