The 90% figure is a pretty fuzzy number at best. And for multiple reasons.
First off, this includes civilians killed by both sides; those killed by accident by american forces and their allies, and those killed by suicide bombers by Al Queida and it's affiliates. The few times american soldiers have targeted true civilians have been few and far between. Also, they're the ones you hear about on the news (Haditha comes to mind, even though that story isn't exactly as it was portrayed in the news).
And second, every taliban fighter and al queida member we have killed is technically a civilian. They are not members of a nations military force and do not wear uniforms. They live among the populace and often times use that fact to hide themselves behind human shields.
Yes, lots of civilians have died. And yes, that is a horrible thing. But the fact is that the number of actual civilian deaths at the hands of American or Coalition forces is a MUCH smaller number than the 90% figure.
Having been involved in both wars, I can tell you that the only difference between a civilian and an insurgent over there is usually the direction they point their gun.