An AP does not mean that the Commander does not have controll over the ship. It is a QoL feature. 95% of all commercial flights on Earth today, are done by computers with Humans at the helm. Humans (Commanders) will take control when things goes south.
Why is this concept so hard for you to grasp? An AP will not be something you turn on and then go to bed... you turn it on and then monitor it. It gives you, as the Commander, an opertunity to reast your hands and arms, but you can't leave the seat; you have to monitor it, but does not have to be "hands on" all the time.
This is actually a reality today in most aircrafts we have... how would this make Elite Dangerous, as a game, worse for you?
Logically it does make sense that AP should be a system available in some ships. Logic and game design don't always go together though.
Given the direction we humans are currently headed towards with self-driving cars and even tractor-trailers, automated transportation will be considerably safer than human drivers. I would think it logical that in the year 3302, all transportation methods will be fully automated and won't need to have drivers or pilots. They would save a lot of resources cutting out the weakest link. I'll go play Elite: Starbucks Barista now.