it's simply very hard for crm to take root in the company. just look at how many of the most senior management pilots are running the show. you can tell an organization by it's leaders.
it's very obvious that the first officers in the tacloban and butuan flights worried more about being "polite" to their captains than the safety of the flight.
think about the fear being instilled by head of a320 training more than sound procedures for the trainees. what happens when a first officer on training faces all these from the beginning? how do you expect the young pilot to behave in the line? speak out? "don't challenge/please the seniors" is instilled, above all. after all, the most senior guys have always said "attitude is what matters."