I am sure that one day automation will replace the pilot, but there are many, many problems to overcome in the meantime.
One of the first questions that has to be asked is why you'd want to do it. Until it can be done more cheaply than it is now, with no loss of safety (or even an increase), then it won't happen. In the overall scheme of things, the cost of the two pilots is not that high - and there will be no manpower or salary savings at all if the pilots are replaced by ground-based operators working to European Working Time Directive limits, so pilotless aircraft will only make sense once all the decision-making and operating is done from within the aircraft by computers. This process must be absolutely robust and incapable of interference from unauthorised outside agencies.
Machine-based decision making is not good, generally, and needs to improve greatly before it can be relied upon to replace humans in the three-dimensional airborne environment. In fact, I could see automatic ATC coming before pilotless airliners! Radio-based ground-air communication is not currently secure enough to guarantee that pilot-free airliners could be controlled from the ground when necessary.
Comparing the civil and military environments is really not very helpful. Military UAVs exist because military pilots cost millions of $, and cannot be replaced quickly. The reliability and longevity of a military UAV is not very important, as they are built down to a minimum cost and in significant numbers. Civilian pilots are cheap, and can be replaced quickly, yet their machinery costs hundreds of millions of $ and must be incredibly reliable, and very long-lifed.
Aircraft coming into sevice now will be still around in 50 years time, or maybe more. No passenger-carrying aircraft are currently in development or proposed which do without a full compliment of pilots. That, to me, suggests that we are looking at a minimum of 70 years before any significant inroads are made into the pilot community by computers! I shan't worry about my job from that angle yet..