Oh, I see. Great article from CNN.
Pre-programmed doesn't mean it was programmed in advance or there is any record now of the programming. They are just assuming from the plane's flight path (do they know the flight path then?) that this could not have been achieved by manual flying and would have to have been flown bya programmed auto pilot. Even re-programming the auto pilot (so the plane does not crash into other planes!) is very complex, and would need to be done by an experienced pilot. Though possibly one who is being held at gunpoint.
I know this is a bit touchy-feely, but I like the pilot from what I've read about him. He sounds quite brave, going against the establishment and sticking up for his belief in democracy, despite the trouble it may get him into.