Basic flying skills won't help you fix that -- if you're over the middle of the ocean at night at altitude in the middle of a storm with strong updrafts and your instruments are giving you strange readings, it can be really hard to "feel" whether you're actually in a stall. Especially if your airspeed indicators had been acting up earlier in the flight, so you knew you couldn't trust that reading. It's ultimately an interface design problem: with new control systems, it's not always apparent what interface will be required in every edge case.
But ultimately, you're right. Flying is so safe now that major commercial airline accidents require 5 or 6 cascading failures in many different parts of the system (maintenance, design, security, pilots, ATC, etc) to occur. Even in the accidents I mention above there were other failures that happened outside the plane: the plane wasn't de-iced properly, or ATC routed them through a storm they really shouldn't have.
I didn't see a single data point that indicates that commercial aircraft are less safe than they were at any previous point in time. With more flights taking off now than 40 years ago and avoidable crashes occurring due to pilot error being few and far between, this seems like nothing more than a guy with an opinion pontificating on a blog as he gazes out his window.