The .air file has those sections in it, but the aircraft.cfg file overrides the .air file if they have different entries.
Here's the section you want to modifiy, from the default 747 in FS2002:
[autopilot]
autopilot_available=1
flight_director_available=1
default_vertical_speed=1800.0
autothrottle_available=1
autothrottle_arming_required=1
autothrottle_max_rpm=90
autothrottle_takeoff_ga=1
pitch_takeoff_ga=8
I think you can guess which ones to change, but I'll tell you anyway: activate the autopilot by changing autopilot_available from 0 to 1. The rest are optional, so I would check other aircraft.cfg from aircraft of the same general type. You could also copy that section of the .cfg over to the aircraft you are trying to modify.
