They were doing what came natural to their generation - holding onto perceptions that had been guiding us since the cold war.
Unfortunately, many of those perceptions, particularly in the Middle East had always been, or had become, based on fictions before the cold war was officially over.
Alliances and allies have never been things of principle to the duplicitous Arabs, particularly the Saudis, and in many cases we had always been more of an ally to them than most had ever been for us - in word and in deed. Also, the WWII and cold war perceptions had masked the full and across-the-board implications of the Islamic fascism, and its growth which began at the end of WWII and was already extensive long before the first Gulf war and the public emergence of Al Queda. There are many aspects of that Islamic fascism that, from its inception, have been fostered and supported by some of our so-called "allies" in the region, with all its anti-western and western-hating aspects.
To put it simply, at the heart of the matter, there is not a dime's worth of difference, from a western perspective, between the political and religious views of Osama bin Laden and the ruling government and ruling Wahabi religious leaders of Saudi Arabia. They mouth the same western-hatred views as Osama in their state-controlled media and in their schools. Their schools, across the Middle East, produce the mush-for-brains cannon fodder of young men willing to go "defeat" the evil west. Wealthy Saudis connected to the Royal family continue to be the largest financial contributors to Al Queda. The Saudi royals do not even actually oppose the terrorism of Al Queda. They only oppose the use of it against them. These are Baker's friends.
Bottom line is until the waring groups in Iraq et al fight it out to an end.... there will be no solution. He can talk about a political solution all he wants, but it isn't a reality.