Where would I put the quibbles? One sensitive fellow detected a protestant bias, but I suspect that is just second hand "whig history" stemming from his sources. Which tended to whitewash anything in the direct lineage of classical liberalism, as it first developed in the English speaking countries.
Thus he mentions the crucial importance of Locke for the development of limited government, which is perfectly true, but presents it as advocacy of tolerance, which is not. Locke had no room for tolerance of "papists", and the sad history of Ireland under British rule, long after England had gone "whig" and took to congratulating itself on its broad minded enlightenment because of it. Which I mention not to pick at old wounds, but merely to point out that we got here by a tortuous road, not by one group of men becoming angels and eventually being followed by everyone else.
Another place I would quibble has to do with his Islamic history, which is considerably "thinner" than his presentation of the development of tolerance in the west. He says there wasn't political diversity or country divisions within Islam. That is not really true. It is more involved than that.
The Umayyad dynasty moved the capitol from Arabia to Syria, while the ruling family shifted, and the Shia split as a result. So did the Khajirites. Eventually the Umayyads were replaced by the Abassids who moved the capitol to Baghdad, which they did because they balanced Arabs with Persians. Then came Turks, and they set up military Sultans over religious caliphs. The Mongols smashed the Islamic east after that, and in their wake the Turks came to dominate the mideast, while the Moguls ruled northern India.
The rest of the Islamic world did not simply go along with this, however, and revolts split away Fatamid Egypt, and seperate again Muslim Spain and north Africa. Many of these developments had parallel religious ones (Fatamids and Shia "Twelvers" rather than "Seveners", Abassids and Mutazilite theology, legal literalism and Almohad Spain, etc).
The general picture is thus not a monolithic unified state with religion and politics united. Instead, they did not really settle the principle of political or religious succession, and factions formed around dozens of views on those subjects. And grew more numerous, accumulating over time. Islam in its most vigorous stage diversified by "secession". It proved easy again and again for a section to develop a different view of religious legitimacy than the rest, and break off as an independent polity on that basis. In theory all recognized the idea of one caliph, but they sometimes disagreed about who that was.
The Turks changed that somewhat, reimposing a greater degree of political unity than had been there before their arrival. That development went along with a state-religion split of a sort, however. Leading generals became sultans, the de facto powers, reducing the caliphs to figureheads, much like prime minister - king or shogun - emperor relations elsewhere. Eventually the pretence was no longer kept up and the sultans became caliphs in name, as well. Still, it was a real and enduring political distinction in the Islamic world. There is the leading military power, and there is religious legitimacy, and they do not always coincide, though sometimes they do.
This point is important to understand later Arab nationalism and the attraction of religious legitimacy for it. Because the leading military power was Turkish, while religious legitimacy could plausibly be presented as an Arab commodity. Indeed, the history of the dynasties is one of old rulers receeding to religious authority as new nations achieve the real military power (Meccans, all Arabs, Persians, Turks).
When the Saudis want a religious basis for the state, it is a way of underlining they do not wish to be superceded by Turks again, on a basis of secular political power. It is not really such an accident that Ataturk was the one able to create a secular state. The Turks rode into Islam late, on the basis of military prowess. It was their "long suit", internally.
The tension between the worldly needs of political expediancy and the more abstract demands of religious legitimacy has been the dominant factor in internal Islamic politics since the Umayyad dynasty, very soon after the time of Muhammad. The same tension is there for a Musharraf today.
Islamic government has been overwhelmingly monarchic. Religion has been the populist principle, countervailing the power of the court by the possibility of any holy firebrand coming along and leading a mutiny. Ambrose Bierce once wittily remarked that absolute monarchy is that form of government in which the leader does whatever he likes, provided it is exactly what potential assassins demand of him. The Assassins were a medieval Islamic sect.
In some respects Islam is set up for limited monarchy, with religion providing the higher law and the monarch simply enforcing it as an executive. That has been the form religious scholars have sought. But rulers have proved more independent minded than that, while populist leaders have substituted secession or conspiracy for elections.
So there is a lot of cynical political unscrupulousness, sitting rather uneasily with competing sectarian religious ideas. It is never entirely clear whether the true believers are using the warlords to impose their theocratic dreams, or the warlords are using the pious blather of the true believers to whitewash their naked power grabs. Usually both, or the decision between them depends on who laughs last - and can be reversed tomorrow. Call that, "seperation of church and state, Islamic style".
I did not say it was promising material. But at any rate, not the monolith of united state and religion that the article seemed to present.