>Yes, but without any direct communication, no organized Air Traffic Control, and without tracking satellites, it seems very easy for ground troops to mistake a civilian transport with a military transport.
not to mention, ground troops in a civ-war-like situation may not have the technology to detect a civilian aircraft's transponder, nor even expect one to be in the area (after all, it's more-or-less a war zone right now).
Except for the transponder...