Automation
Just compare aircraft to trains for which technological requirements which are a lot less complex. How many fully automated trains are currently in service? Not that many, and the ones in service are only used on smaller routes. There will always be some limited form of human input necessary, especially for non-normals that required some limited 'out of the box' thinking. It would be virtually impossible to design an automated aircraft to take care of all kinds of possible scenarios. Just look at that recent ditching in the Hudson river in NY.
Even if it was possible to design such an aircraft, don't forget that for both airlines and aircraft manufacturers, it's probably a lot cheaper to have a human pilot in the front instead of just an automated pilot.
The key word here is liability!