As operation becomes easier, training can also become easier and, more importantly, cheaper. This results in less rigorously trained pilots. Also, fewer people will fail an easier training program, resulting in pilots with less natural talent making the flight deck.
Modern aircraft are extremely reliable, but the AF447 incident (http://en.wikipedia.org/wiki/AF447) showed that when the automatic systems fail, in this case due to iced-up pitot probes, the humans in the loop failed to control the aircraft resulting in hull loss.
The Wired article points out the differences between the Airbus side stick and Boeing yoke, additionally with Boeing the autothrottle physically moves the thrust levers. But pilots with thousands of hours flying benign routes are considered experienced, yet are also unable to recognise a stall, a fundamental hazard to safe flight taught very early on in flying training.
The issue seems to be an incongruence as technology outpaces training.
On AF447- "Pilots a generation ago would have done that and understood what was going on, but [the AF447 pilots] were so conditioned to rely on the automation that they were unable to do this. This is a problem not just limited to Air France or Airbus, it's a problem we're seeing around the world because pilots are being conditioned to treat automated processed data as truth, and not compare it with the raw information that lies underneath." William Voss, President, Flight Safety Foundation (http://www.guardian.co.uk/world/2012/jul/05/air-france-crash...)
Great aircraft, lets hope the training keeps pace.