Pilots make important decisions when something unexpected happens.
Automation is a good thing to have as an adjunct to the pilot if the flight is fairly normal.
Hijacking and violent or biligerent passengers are common occurrence. Pilot usually has to deal with the hijackers with a main concern of protecting the lives of the passengers. This very important minutes or seconds that the the pilot makes to protect the lives of his passengers can not be provided by automation. I saw in the news last year when one passenger went inside the cockpit and tried to take control. In a commercial airline, they need one person to make important decisions in case of emergency and that's the pilot.