i am running arduplane 3.9.3 on pixhawk cube 2 my throttle works normally in manual mode and fbwa on ground but when i switch to auto mode or rtl throttle of plane closes itself while being on ground i tried changing home location but still throttle remained closed i cannot risk a flight without being sure about it
That is normal behavior. I manual and fbwa the throttle is directly controlled by the pilot. In all other modes the pixhawk controls the throttle and it knows it is not flying so it doesn't run the motor, with the exception of an auto takeoff command. With a new plane you should take of in manual mode and get to a safe altitude before trying other modes.
i am using engine based plane so i am worried about flying it in auto mode in air what if throttle gets closed and plane crashes
If the throttle/engine works in manual mode it will work in auto. Have you set up your ICE_ parameters yet. That may be it. The behavior I described is for an electric plane. With an ic engine you would start it in manual unless you have an electric starter. I am not sure of the exact behavior with an ic engine, but if you don't have the parameter set for ice then it will not run when not flying in auto mode. Check your parameters again and take of in manual mode. If you are not able to fly in manual mode then you should not be flying ever, until you have learned. Seek help from an experienced RC pilot.