I think you are absolutely right...
...that it is only a matter of time until automation totally takes over. I'm not saying that I am comfortable with it; just that it's inevitable.
Even with today's capability of automation, the argument for pilots on board remains as it always has been for the last 20+ years; to be a backup for when the automation fails. But in recent years, we've had a spate of major accidents where pilots flew otherwise flyable airplanes into the ground because they lacked basic stick-and-rudder skills. Air France 447 and Colgan Air 3407 good examples. The Colgan Air 3407 crash was the primary impetus for the new 1500 hour and fatigue rules. (IMHO, the fatigue rule change was long overdue)
The question is: If the purpose of having pilots aboard is to save the day when the automation fails, but poor stick-and-rudder skills preclude them from saving the day, then what is the point of having them there?
Conceptually, getting rid of pilots altogether would be very appealing for the airlines. The two most expensive employees on each flight are eliminated. The space traditionally occupied by the cockpit becomes available for more seats. And with no cockpit to storm, it makes taking over a plane less possible for terrorists.
Of course, the current generation of air traveler can't and won't conceive of or accept the idea of being a passenger on a "pilotless" plane. But that will change over time. Automated military drones are now accepted my many without a second thought. Soon, we're going to have automated automobiles sharing our highways. And within 20 years or so, they will no doubt have an accident rate that is far below what conventional cars have. The next generation beyond us will not question automation the same way we do. They'll accept it. And when statistics show that more accidents are due to pilot rather than mechanical error, they'll be comfortable with it.
I've been telling my commercial pilot friends for some time now that their profession had better improve the skills problem, otherwise, within a generation there will be no reason for their existence.