I really don't believe he got "directives". What he likely got was suggested talking points to be used when meeting with heads of Arab nations. What you are not hearing, he probably also got suggested talking points when meeting with Isreali officials too, and talking points for any specific agenda items we have with our closest allies.
It's not unusual for the State Department or the NSC to provide talking points to the Department heads to use when they are meeting with specific heads of state to further US national security points. That way, the foreign heads of state get a consistent message as they meet with senior US officials.
Clearly, for better or worse, the Administration is trying to drive home the point that we are not at war with Islam, but at war with the terrorist factions. I don't think it is particuarly onerous to do this. Of course, if you want to twist anything that this Adminsitration would do to a negative point, then of course you can. Just like the left twisting Bush's actions to their negative point.