Did you check all their settings?
Just for personal opinion, i prefer to defend it by soldiers, as they get nice experience without need to hurry for civilian protection (several AR snapshots give more experience than long burst).
Edit: Uh, i remembered my first experience of using SAM inside base with ufoai-2.4. When i set it to attack only ufo, attacking base, it did not work, so i had to set it to attack everything.