Answer to your question lies in various layers; but i will go for the basic only: anarchy and rebellious attitudes do not originate in vacuum, rather they are rooted in indigenous soils, and for the most part soil tillers are to blame for promoting the game of warring by showing shamless power as the supreme logic and ethic.

Pakistani state doesnt ever show reflecting or respecting the commoner’s aspirations, rather through enlightened PIRATES it always showed least prudence. Take the example of miltary take overs, brazen sale of justice and disrespect for rule of law. If Gen. Zia islamizes, Mussaraf modernizes. If Zia says constitution is nothing more than a piece of paper, Musharaf demonstrates it by sending 60 judges home with a stroke of pen..Political elte is no exception, wherein the most corrupt and unruly decide the nation’s future. Politicians dont hesitate in siding with anything that may benefit them. In karachi on 12th May scores of people are butchered by a pressure group, and the then chief of army staff congrats it and the rangers deputed in karachi turn a blind eye to this massacre.
If these are the grim realities here Baitullah Masud and his likes are not expectd players. To cap, Pakistan as a state not on a single occasion succeeded in proving that it is meant for people, so, deflowering it by the militants is understandable, if Masuds protect Baitaullah it shows they dont trust the state, so, the state, its lusty and blind folded generals, political elite is to blame first that alieniated the people from nationalsm, then we can think ofg saying a word against the BLA, Taliban and anyother so called separatist or terror groups.