They reported this morning that they used a disturbance in the plane reported by the flight attendants to get the pilots to come out for assistance. After they got access they took control of the flight with their own trained pilots.

They told everybody that they had a bomb so as to keep everybody from attacking them. Since the people on the plain had no idea what the actual mission goal was then they didn't resist as much as they could/should have.

Too damn bad but in this case you couldn't really have expected them to do anything different with what they knew at the time. For all they knew they were just gonna end up in Cuba or the Middle East and everybody would end up living.