What's The Confusion Here?

From CNN:

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The Guardian Council in Iran, the constitutional body that examines legislation to be sure it doesn't conflict with the constitution, issued a statement saying, in part, that the statements "emanated from [the] pope's ignorance about Islam."

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On Sunday the pope said he was "deeply sorry" for the reaction to comments he made last week when he quoted from a 14th-century emperor regarding Muslims.

"These in fact were quotations from a medieval text, which do not in any way express my personal thought," he said in his regular Sunday blessing, the Angelus.

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The remarks came last Tuesday, when the pope spoke to professors in Germany and quoted 14th-century Byzantine emperor Manuel II Paleologus.

"Show me just what Mohammed brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached," Benedict quoted.

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The killing of an Italian nun and her bodyguard Sunday at a children's hospital in Mogadishu, Somalia, raised speculation that it was carried out in reaction to the pope's remarks on Islam. (Full story)

In addition, Palestinian security sources said a church in Tulkarem was attacked Sunday with Molotov cocktails, and there was an attempted attack on a church in Tubas, near Jenin.

Authorities were also investigating Molotov cocktail attacks on three churches in Nablus on Saturday, as well as an attack on a church in Gaza.

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Would some astute observer explain all that to me? The Pope was just quoting some old text to a bunch of academics. And THEN, turns out the guy he was quoting might've been right.

So what am I missing here?