The main difference between manned aircraft and unmanned drones killing civilians is accountability.
How do you hold anyone responsible when you've no proper way of identifying who was controlling that drone, or indeed if it was being actively controlled at all. How does innocent Afghans seek justice after death strikes from above and you might not even have been able to identify the aircraft the bomb or missile came from?
You can't bomb yourself to victory from the air, it didn't work in Vietnam in the 60s and 70s, it didn't work for the Russians in Afghanistan in the 80s, hasn't worked for Israel in Gaza or the West Bank for decades now (and not for lack of trying!), and it's not going to work in Afghanistan now either.
Every village blown up by drone strikes is just going to turn even more Afghans against any and all foreign troops on their soil. Lame excuses like "it saves American lives" is just idiocy; a soldier that's scared to die shouldn't have joined the armed forces, and a commander that isn't willing to risk his troops is spineless and incompetent. Risking one's life - hopefully in a righteous cause - is a soldier's job. When you start blowing up villagers to save the lives of soldiers then you've already lost the battle.
Also, the people targetted aren't "terrorists" by any legal definition of the word. At best they're SUSPECTS, and proper western tradition is to treat suspects as innocents until proven guilty in a court of law. It's NOT proper tradition to blow suspects to kingdom come just in case they might be guilty of something, together with anyone who happen to stand nearby.