Some may call drone strikes terrorism but I do not. In my mind the difference is intent.
"The road to hell is paved with good intentions."
I can hear an al-Qaeda leader having the same debate in his head. Okay, he's more radical with what he thinks is the solution to the damage inflicted on Islam by the US (e.g. "corrupting" the minds of the Islamic youth). But that's why he's a radical. To his own twisted mind, his intentions are "good".
Other posters have already mentioned the way the founders of al-Qaeda (or maybe al-Qaeda itself in an earlier incarnation) received assistance from the US military. The intentions at the time were arguably "good", stopping the spread of Soviet influence in countries like Afghanistan.
Ultimately, it's the consequences that matter. When drone strikes or nuclear bombs kill far too many civilians, then maybe it's time to change the means, the tools used to carry out your intent.