So if you listen... they actually do explain it all at the end.
Mega-Spoilers here...
So after Bobby "flies away" in the flyer, they eventually go back to Tom Hanks. Who again reiterates the point that he tells it differently then it actually happens. As he did at the begining of the movie. So after he tells the kids that he changed the story, they look at him gravely. Since they now know more about what happened to their uncle Bobby, and that Tom Hanks is a little crazy. Anyway, Tom Hanks is very sad and still again telling about changing the story (why would he be that sad if the kid got away and they still wrote eachother... and wouldnt they have gotten together by now if they are both adults and away from the king?) plus why would he have to change the ending that much if he got away and writed him? What would he change?
After the impossible flying away sequence, everyone looks sad and Hanks says...
"Now do you understand what I meant about history being in the mind of the teller?"
His kids say "yes", and Tom Hanks replies, "cause that's how I remember it."
Why would he make such a point of telling about changing the ending if he got away? What would he change if he actually got away? If him getting away in the plane isn't the changed element in the ending... what is? It's really easy to see what happened via Hanks' ending segment. Bobby died in take off... why in take off and not before? Keep reading...
But here is the big thing. The kids sadly ask if they can ask him a question which they know will be hard and he replies... "yes"... and they say "Is that where we got Sampson (the turtle)?" And Tom Hanks sadly, breaking his little fantasy, says "Yes. That's where we got Sampson."
So they got the old turtle(cause turtles live for a long time), the children have Sampson the turtle.
How would they get the turtle if it flew away with Bobby? Would Bobby mail it back to them? No. Bobby crashed the flyer on lift off... and died... the turtle... protected by its shell and its box... lived... and Elijiah Wood took it and kept it. When Elijiah Wood grew up into Tom Hanks (wow. never thought I'd say that), he kept the turtle and the kids now know where it came from. He never told them before.
So the kids found it so hard to ask him about Sampson cause it went against his little story of Bobby and Sampson getting away. The kids have the turtle that they wouldn't have gotten if Bobby's flight had worked and the turtle and Bobby flew away and were never seen again, plus if Bobby had lived... he'd have kept the turtle himself..
The kids know Bobby died, Hanks knows Bobby died, and we know Bobby died. The ending cleares up all questions. The feelings of the scene, the lines that are said, and Hank's "changing the story" lines all tell the end. But the Sampson thing is the key to the truth. Gives it all away.
Thank you.