Salibi:
I don’t know if they all went. But look at it from their perspective. They could either join a religion that was similar to their own, or continue to be persecuted by the Orthodox. Their choice was probably, er, helped by the fact that they would have avoided taxes or death if they converted to Islam.
So why do modern Copts not view Islam as a religion similar to their own (in my experience at least)?
Well, let’s be clear here. Some Miaphysite and Arian groups certainly did convert to Islam. The vast majority of Christians in the Middle East and North Africa did, whether out of fear, out of benefit (no special tax) or because they viewed Islamic theology as much closer to their own than Chalcedonian Christianity. But for many Christians in those areas they in fact did not fight the Islamic invaders simply because under the Islamic rulers they treated with a great deal of tolerance, as opposed to how they had been treated by Roman and Byzantine authorities.
The Copts were persecuted by the Byzantians in the 5th century after they rejected the Council of Chalcedon. Christology was the issue of the time. Once Christianity had become the state religion, the underlying struggles between various Christological formulations, which had been going on for a couple of centuries, suddenly bubbled over as the Emperors, wanting a single Orthodox Christianity for the whole Empire, essentially viewed any group that rejected all or part of any of the Councils as dangerous rebels.
The Copts, in fact, were the majority population in Egypt for centuries after the conquest, and were treated fairly well by their Muslim rulers. There was no need to convert. They weren’t harassed in any significant way for much of their history being ruled by Muslims. So long as they paid Jizya and were loyal citizens, they were free to practice their faith.
Don’t confuse the modern post-Ottoman Arab nationalism with how Islam and Christianity (and Judaism as well) coexisted for centuries. Copts now are, sadly, the targets of much hatred by Islamists, but Islamism itself is a modern creature, at best no older than the rise of Wahabism in the Arabian Peninsula. Islam taught tolerance of other faiths, in particular the religions of “the Book”. Not that there weren’t abuses, but when people complain about the perceived evils of Islam, I often say “Where would you rather have been an Arian in the 8th century or a Jew in the 12th century, Madrid or Paris?”