As Matt indicates, the threats are real and potentially catastrophic should AQ or its affiliates get a hold of weapons of mass destruction. The issue for me is less the high priority being placed on countering the threat than the manner in which we are countering it:
1) too much emphasis on and too prominent a role for the military; 2) the tendency to try to impose counterterrorism as a priority in countries (particularly in Africa) where the governments and people are faced with much more pressing threats from HIV/AIDS, poverty, corruption, organized and other forms of crime, and lack of development; 3) the tendency to want to put a “counterterrorism” label on policy initiatives (e.g., related to education, development, the training of law enforcement officials) in countries where doing so may lead to resistance on the ground and thus be counterproductive to actually countering terrorism; 4) the continuing pattern of exaggerating the extent of the al Qaida connections with what may be local insurgencies, for example in Indonesia and The Philippines, and where labeling such insurgencies as al Qaeda-related may magnify the profile of smaller unrelated groups or stifle attempts to address the local grievances that are motivating the insurgencies (See, e.g., Amitav Acharya and Arabinda Acharya, “The Myth of the Second Front: Localizing the “War on Terror” in Southeast Asia,” Washington Quarterly, Autumn 2007); and 5) the failure to build the alliances and strengthen international cooperation with traditional and non-traditional partners around the world.
Thus, what is needed is not a de-emphasis in terrorism relative to other national priorities but a more nuanced and less blunt notion of what we mean by “counter” terrorism, taking into account the five concerns/limitations I have outlined. I am sure I have left out many others that need to be taken into account as well and look forward to others adding to this list!