So you pulled out one story regarding an airstrike 3 years ago and a protest. Where are the "thousands of airstrikes" you talk about with the resulting many civilian casualties?
Addressing the incident, firstly the militants were hiding amongst the people in the village when the airstrike struck. The airforce since then has changed its operating procedures and such strikes are no longer conducted in any built up areas due to threat of civilian casualties. Villages are now evacuated and operations conducted.
If there was such anger against the operations we would literally see civil war in the region. The fact is the tribes are on side as are the people, in region notoriously infamous for waging war on anyone who threatens them. Ok let's say that armed mass rebellion is stretching it a little far where is the civil disobedience then? Where are the hundreds of thousands walking in protest in Peshawar? Where are the huge rallies decrying Pakistan and the evil strikes they have done? Where are the shutdowns and I can go on.
As for the protest link, I'll quote the article when it state there was some "aerial firing", unlike your forces who use protestors as target practice and shoot to kill.
The last report is an amnesty study which deals with extra Judicial killings and torture of suspects. The report outlines that some of the detainees do not make it out, whilst the vast majority do. Even that is wrong but the report clearly outlines the difficulties in fighting these brutal insurgents "Amnesty acknowledged the challenge Pakistan is facing in fighting the Taliban along its border with Afghanistan". The report does hold value but then it is based according to their own words the report was based solely on testimonies, "more than 100 testimonies from victims of human rights violations in detention, witnesses, relatives, lawyers, Pakistani officials and militants.". So there is a question of accuracy here. If people were to go to Swat, the tribal areas and ask locals what they thought of all the "human rights abuses" many would say that didn't care and that the militants deserved it. Again that's not a benchmark for us and any wrong should be investigated.