The problem is you are probably playing the mission on normal. Easiest way to destroy it is to change the difficulty to hard before the mission. On normal, the actual target for the cockpit is the windows on the topside, which is virtually impossible to hit except at a certain angle. On hard, the cockpit target is underneath hanging down inside the tunnel of the Aigaion, and is way easier to hit if you fly towards it from the front.
Just go into your settings before the mission and switch the difficulty to hard, then after you're done, switch it back to normal for the rest of the campaign.