I think the costs of making and running an unmanned aircraft for cargo or passenger carrying exceeds the costs of having a pilot. There was a recent study showing that it cost less to patrol the border with a pilot and single engine airplane per hour, than it did to have a UAV do the same work.
These unmanned aircraft require much larger ground crews (means employing more people, means paying more people, costing more money overall), than would be required if you had a pilot. Further the risks involved are much greater when you talk about hacking and jamming.
As people have mentioned earlier, autopilots act weird, they shut off at random times, etc. That's unacceptable if it is the only thing flying the aircraft. Rick mentioned it happened about twice a month, no big deal, doesn't really need much work done to it since you have two pilots there who are more than capable of flying it by hand. The fact is it would be costly and difficult to fix that problem, something that would be required to be fixed if unmanned, possibly grounding whole airworthy fleets for undetermined amounts of time.
Also computers crash, they crash all the time, sometimes for no apparent reason at all, its no big deal, but when its the only thing flying the aircraft it becomes a big deal.
Further let's look at some other modes of transportation, you got automatic elevators, trains still have Engineers, boats still have Captains, and cars still have Drivers. Those would be automated first, prior to aircraft, due to the simplicity of it, dealing with less dimensions.
The Pilot isn't there for when things go right, the pilot is there for when the **** hits the fan, when judgement and experience count, something a computer lacks.