Yes, the doctrine is working to accomplish its goal, which is not that there would be democratic governments in the middle east. "The responsibility of the United States is to protect itself and its friends by promoting democracy where the terrorists are located so as to undermine the basis for terrorist activities." The goal is to undermine the basis for terrorist activities.
Iraq is going to fall to a civil war within moments of our withdrawal - spent enough time there, talked to enough local leadership, and they know it too. Our policy is to seek out, close with and pay off the enemy, by contract or humanitarian aid. Do you have any idea what the policy of hiring local contractors has done politically and economically? Or the millions in COMREL we spent? We bought converts. Afghanistan has the same potential, different players and it will look a little different but same result. Neither country can now, nor will be able to in the future, sustain support to terrorist activities at the levels prior to the Bush doctrine. People in both countries want democratic capitalism now, and they will hash it out violently just as we did ... with help from outside countries I'm sure ... just as we did.
Not only that, but the growing influence of democratic ideals in the region has successfully penetrated the minds of the young people in Iran, as we see on TV right now, Also destablizing/undermining Iran's ability to participate in terror as they have to focus inward. Think of the young Iranian guy who was killed in a cross fire - 19 years old on his way home from acting school. Not on his way home from terrorist indoctrination ... acting school. Search some of the Iranian Youth blogs ... drinking, sex, drugs, rock-n-roll. We've promoted good ol' Americanism big time over there, which undermines the basis of terrorism.
No one said it would be clean, elegant or pretty.