****SPOILERS******
After watching the 1st episode again, I was pretty sure the pilot/dad is not one of them, and the second episode confirmed that.
So its still up in the air as to who the prisoners are, but I am leaning towards future-humans who have evolved or had their DNA modified.
As for who blackmailed the pilot into flying the plane into the Prez, I am still clueless, and if Sophia's people on the outside saved the Prez and transported the plane to the desert, was it the assassin group who came in helicopters to kill the passengers? Or Sophia's ppl?
I shouldn't have deleted episode 2 after only 1 viewing