I think you are looking for:
$query="UPDATE `FlightSchedule`
SET delay = CEIL((UNIX_TIMESTAMP(time1) - UNIX_TIMESTAMP(time2))/60)
WHERE `flightNum_arr`='".$flightNum_arr."';";
Alternatively, there is TIME_TO_SEC function - and, since it provides result in seconds, you'll need to divide it to 60 too.