What do you make of the attacks of the Muslims when they defeated the Persians, and the when they spread accross the world under Caliph Omar r.a.? [and in later history as well]. When the Muslims attacked Khayber etc? Not all the wars faught were defensive.
You are confusing Taliban with Al Qaida. The innocent people also, please name them.
Were the people Taliban killing in Afghanistan, non-muslims? Are you comparing Taliban to Omar (RA) and the Muslim army which conquered non-muslim empires. Are the Swat militants bravely establishing a new "Madinah" among hostile anti-Muslim Kafir Pakistanis? lol
Now when they are doing the same thing [trying to kick the occupiers of Afghanistan out] the government is hitting them as well. They are doing what they were taught to do [and that too by us] i.e. fighting those killing other muslims [right or wrong] and people now don't know what to think of it.
In Afghanistan they were killing other muslims for many years. They were fighting for power. Mujahideen lasted only as long as soviets and communist rule existed. After that it was intra "mujahideen" warfare.