Its not the Taliban as a military force that is a threat today, its their ideology. True that taliban isnt much of an existential threat to Pakistan than say it was apparently a couple of years ago. However, the spread of ideology which drives the taliban is what is troubling.
Considering the recent turn of events culminating in S. Tasser's assassination and the shocking support shown by many an educated and well-to-do Pakistani to the assassin gives a glimpse into the decay thats being setting into Pakistani society. This very religious ideology, while formed the basis for Pakistan' creation, a fundamentalist ideology version now being followed threatens to destroy the very fabric of Pakistani society and the country as a whole.
Consider the parallels with extreme left-winger support to naxalite ideology in India. Naxalite movement survives not because of the poor, but because of the support of some (pseudo)intellectuals drunk on such an ideology. Fortunately those are few and far in between. Take that out, and you will see the naxalite movement wither away.
Same with the taliban. Its the ideology which drives such extremists - here a skewered interpretation of Islam, basically religious! The ideology which finds support among an intellectual/working class with sinister/ulterior motives or an axe to grind - in this case anti-US sentiment or power in Pakistan. How do you counter that ideology, its up to you.