Autopilots are great at controlling a fully functioning aircraft, and can do so better than a human pilot. But are not designed to react correctly to a myriad of abnormal situations which ...
I recall watching a program on the gogglebox some years ago that was talking about the issues faced by pilots when "something's broken". For example, in the Sioux City DC10 incident, the pilots ended up flying he aircraft with just the two remaining engines - they were fortunate in having a training captain on-board who managed this for them and took some of the pressure off the situation.
Anyway, modern airliners can use alternatives to the traditional control surfaces - eg some of them use spoilers instead of the ailerons. There has been talk of training computers to use "whatever is working" - and I recall them saying that some simulator trials had shown that the computers would often manage to fly an aircraft that the pilots couldn't fly.