Ben was tied up before the rescue so it makes sense that he was taken off the island. As r.palmtree noted, he has died and Jack is upset because Ben was the last link to the island.
Ben knew that Naomi was lying because he remains in contact with the outside world and saw the coverup of the found wreckage; understanding that someone is now secretly searching for the island.
Fountain of Youth makes perfect sense. Y’know, Jacob’s Well. Locke will now take Bens place as leader of the others. Something Ben knew would happen but could not prevent.
Wow, that makes a lot of sense.