The reason I have autotakeoff turned off is that it is more realistic that way. Taking off and landing are major portions of flying an airplane, so I like it to be a part of my flying in Aces High, too.
Other advantages might be (not sure, since I don't fly with it on) that you can maneuver better on takeoff when your field is being capped/vulched. I go to fields that are being swarmed by the enemy, take off from the hangar, and use the rudder to maneuver, barrelling out of the hangar in some direction that is less expected, still working to get airborn as quickly as possible, but then staying maneuvering right near the ground just after lift off. That might not be possible with autotakeoff turned on.