A view from the design office....
I suspect strongly that the job of the bomber pilot is on it's way out for most roles, there may well remain a role for certain types of local ground attack - the Harrier / Apache role, where close-in identification and decision making need to be made in real time. The death of the fighter pilot was forecast in a well publicised UK government paper in 1957, and hasn't happened yet. Again however, I think the role of controlling an aircraft, controlling the weapons, rather than dogfighting is almost inevitable - so the machines will start to take the main risks more and more.
I doubt very much that the job of transport pilot will ever die - but it is already becoming much more of a management role and less of a hands-on role, and I suspect that won't change. Who will ever want to fly as pax on a totally automated machine? Who will make the decisions on diversions, throwing pissed pax out the door, etc?
I can't see any way in which certain flying roles can ever be totally automated. For example - SAR, small local transport routes between semi-prepared strips in the back of beyond, sightseeing - and of course flight testing the non-automated aircraft.
So far as I can see the jobs of both pilots and engineers can only get more interesting. Except for that of airline captains, who presumably will continue to be paid more than anybody else for reading page 3 and occasionally checking the dials or dealing with a badly behaved passenger to relieve the boredom.
G