Thanks for the links! I think the article assumes a passing familiarity with all that history. It is in line with the Economist's style in general, and is really a necessity for them to provide their type of content without every issue becoming a history primer. Although a "background material" section would be pretty neat for them to include.

And you cannot understand the "tolerant" period in the middle east without realizing that that period happened with a partially muslim government, but with the society very much an eastern roman society.

1) Barely any muslims at all. The actual society was near 100% Christian at the time with small concentrated pockets of Judaism, and a muslim army concentrated in the capital.

All of the organisations that made the golden age happened, almost without exception, were Roman organisations that existed before the muslim invasion and got more freedom to operate. It ended they started getting systematically killed.

Even so, immediately the dhimma system was introduced. If that's what people call tolerant, then why not say that Nazis were very tolerant of the Jews ? It's essentially the same thing.

2) Even so, this muslim government itself was not tolerant, given for example it's treatment of institutions of learning. Yes they did not just go out and directly destroyed all of them, but ...

  In 642 AD, Alexandria was captured by the Muslim army of Amr ibn al `Aas. Several later Arabic sources describe the library's destruction by the order of Caliph Omar.[34][35] Bar-Hebraeus, writing in the 13th century, quotes Omar as saying to Yaḥyā al-Naḥwī: "If those books are in agreement with the Quran, we have no need of them; and if these are opposed to the Quran, destroy them."[36] Later scholars are skeptical of these stories, given the range of time that had passed before they were written down and the political motivations of the various writers.[37][38][39][40][41]

While the library was notorious for political interference, keep in mind that it recovered from every attack except this one, mostly because the previous destructions of the library did not involve a massacre (they were not bloodless either, but there is a large difference). The muslims killed everyone they could find in a large area around it before burning it.

Muslims, during the golden age, made a habit of killing scientists. Yes there were a lot of scientists during that period, but to say that the muslim part of that society tolerated them is stretching the truth beyond recognition.

3) Massacres were very likely a common occurence. While not much history is known from that period from Egypt), this is from Spain, same government (more or less), same time period, same "Golden age" :

http://en.wikipedia.org/wiki/1066_Granada_massacre

This is not an isolated incident in Spain, but a constant during that time period.