The actual hard part is dealing with emergencies. It's impossible to anticipate and code for every possible failure mode, but an experienced human pilot can sometimes figure out a good solution from first principles. In the famous case of US Airways flight 1549, the pilots intentionally disregarded part of the official checklist and improvised a new procedure on the fly. Would an automated system have performed as well?

The military is willing to accept a certain amount of operational losses in order to accomplish their mission, especially for unmanned aircraft. Tolerance for losses on commercial passenger flights is virtually zero.