This behaviour is intended. If starting a flight in mid air, the sim sets the AP to ON. This was introduced in patch 2 I think and is intended (I believe) to help you take over control of the plane when starting in mid air more easily. It avoids the plane nosediving as soon as you press the FLY button. So once in the plane and oriented and ready to go, just disengage the AP. This is the same fix that stopped the AP being disengaged when using the “travel to” function for the same reason.