How can they protect civilian ships if they can even protect themselves?
Actually, the aircraft carriers in “UFO2Extraterrestrials: Shadows over Earth” won’t be aircraft carriers per se, but a kind of heavy aircraft-carrying assault cruisers with a VTOL system and they will be armed with missiles and other defenses against numerous disc shaped enemies. These defenses will help protect the cruiser. However the main weapon will still be your Fighters. Maintaining fighters on your aircraft carriers will enable them to reach any endangered civilian ships that much faster.