While I have not read this particular accident report yet, I have read much about it in various locations.
One of the biggest issues is the question of how could the captain have been so foolish in pulling the control column in response to the stall warning. In this case, he was pulling hard against the stick pusher.
It seems so obvious that one should not do this and one does wonder how it can possibly happen but reading a couple of articles makes me wonder if there some sort of an instinctive reaction that at least some people have to the stick pusher being activated?
A couple of recent articles in Flying Magazine have made me wonder. The first one said
"Strangely, however, the captain was not the only one who had ever responded to a stick pusher or shaker by pulling back. In 2004, an empty Bombardier regional jet was on a repositioning flight when its crew decided to let the autopilot take it up to 41,000 feet. While the two pilots joked around, the airplane got slower and slower as the autopilot attempted to maintain the programmed climb rate. Finally, the airplane stalled, and the crew reacted to five stick-shaker and four stick-pusher activations by pulling harder on the control column each time.
In 1996, a DC-8 with an inoperative stall-protection system crashed when it stalled at 14,000 feet during an evaluation flight and the crew applied power but did not lower the nose. But what may be the most egregious case on record involved an MD-82 in Venezuela. It stalled, for reasons that the NTSB does not make clear, at 31,000 feet, and the crew held nose-up elevator, in spite of a “Stall! Stall!” aural warning and continuous stick shaker, for a minute and 46 seconds before impact.
Ultimately, the NTSB concluded simply that what happened on the Colgan Air flight just happened"
Aftermath: The Mystery of Colgan 3407 | Flying Magazine | The World?s Most Widely Read Aviation Magazine
With the exception of the DC-8 which I believe was stalled in a nose-down attitude, all these aircraft have pushers and all seem to have pilots fighting them. Perhaps it is a natural instinct to hang on and pull back when the control column is being forcibly moved forward.
Another article in the July issue of the same magazine says
"It is astounding to me that before this accident, Colgan Air did not include shaker and pusher activation in the training curriculum for the DHC-8-400. This is especially surprising because at least one check airman stated that 'most pilots who were shown the pusher in the simulator would try to recover by overriding the pusher' just as the captain did when the pusher activated in the airplane."