While Krauthammer largely points to the danger of the transition of political Islamism for military Pan- Arabism, his points are spot on. He points out the rather thin liberal base and the popularity of political Islam. this reality is reflected further in the polls as two thirds of Egyptians would like Islam to play a greater role in politics. however, there is a great drop in Egyptians who would like a closer relationship in politics as before the Arab spring, more than 80 percent wanted Islam to play a greater role in politics, which, depending on your viewpoint, represents progress.
Krauthammer notes a potential cause for this demand by citing the military in many countries in the middle east rather brutal suppression of any dissent, especially from political Islamists during 60's onwards. This suppression led to a radical change in tactics from opposition groups such as the Muslim Brotherhood who turned to acts of terror in Egypt to get their message across and led to the Islamic revolution in Iran which still stands strong.
This will lead to some serious ramifications for the US in their efforts in creating stability in the middle east as they are largely unpopular in countries most affected by the Arab spring as the policy of containment used by the United States during the cold war is largely responsible for the repressive regimes which gave cause for protest in the first place.