one way of looking at this is as a conflict over which state model is seen by the united states as functional these days--a relatively centralized state with a high degree of control, typically exercised indirectly (the american model) although there's no problem with old skool state of emergency-driven ugliness (egypt for example, with respect to political dissent). more decentralized or fractured states are apparently not able to co-ordinate action to suppress Problems from the american viewpoint. in the conflict region, afghanistan, pakistan and yemen have this structural situation in common. so much for federalism i guess.
this article talks in a bit of detail about al qaida in yemen:
Yemen is fertile territory for extremism as it tears itself apart | World news | The Guardian
and this outlines the dynamic of us involvement in yemen over the past year:
Al-Qaida: US support for Yemen crackdown led to attack | World news | The Guardian
the second is pretty interesting in particular.