The motives are clear. The Bush administration has an interest to exploit this JFK story as means to show the "progress" that they have made in protecting Americans. If they can successfully link the magnitude of this potential attack with 9/11 or somewhere in that neighborhood, they could stir up some support and show the need for protection - - Should they not?
Let's follow the critic's line of thought in this JFK terror plot. Assume that these "terrorists" were under capitalized, had unrealistic goals, and were really only in the planning stages. Who does it harm if the media or Bush slightly overplays the likelihood of the attack and its magnitude? Why would we ever want to consider allowing someone to move beyond the planning stages of an attack however implausible?
It is unfortunate that most people are not drawn to positive news. Fear is what pulls the most weight. Obviously if abused, using fear as a tool is inappropriate. In this case, the media may be guilty of "grasping at straws" to make this about a serious terrorist plot. However, a little "fear-mongering" might be in order to reawaken Americans who may have become complacent to the unfortunate realities of our world so that we may better protect ourselves.
I want to clarify that I am not advocating more deployment into Iraq or other parts of the world. That has been a losing strategy. My main intention is to show that we need to become aware again of the risks that we face even if it should come from an implausible "desperate for terror" plot.