If they did not, what could Pakistan do about it? The U.S would do so anyway covertly, and the Pakistani government would be seen to be weak, since they were powerless to stop it.
So the Pakistani government 'allows' it to at least appear in control.
They have nukes. They could easily institute a defense doctrine of nuclear retaliation tomorrow, and the terror would stop. But the reason they don't is that they are bought and paid for, both as a country via foreign aid and as individual government members via bribes (or "speaker fees", as you guys call those now).
Let's run with that thought. Let's say Pakistan committed to using nukes in retaliation for US drones shooting their citizens, what are they going to shoot at exactly?
They're supposedly developing longer-range capability capable of hitting some of Europe[1], but right now they might be able to hit some US military bases in the middle-east[2].
I'm not saying Pakistan isn't corrupt, but pretending that they could simply switch from their current US-friendly policy to a strategy that's openly adversarial to US-interests seems to blatantly ignore the realpolitik of the situation.
The U.S. pays the Pakistani government for the right to use drone strikes against innocents who are prescribed as terrorists by a computer algorithm, which encourages hatred and fear and creating the very terrorists justifying U.S. giving the money for the Pakistani government to buy weapons from the U.S. to field an army to fight a war with.
