*** Spoiler Alert ***
What I got from the end was that to "get off the island" you had to atone or redeem yourself for your sins when you were alive. Is it possible that Whitmore, and the guys on the plane, hadn't done that yet?
I think that they were dead from the first episode. I say that because Jack laid down in the same bamboo forest that he woke up in in the first episode. (I could be wrong, but wasn't that dog licking his face in the first episode as well?)
Maybe something happened to Hurley and Ben on the island after the last episode because Hurley said "You WERE a good number 2" to Ben, and Ben said "You WERE a good number 1" to Hurley. Which makes me think that they stayed on the island for a while after, and whatever they did to redeem themselves at that time got them to the church. I distinctly remember someones awakening (Jack's maybe) where he was seeing images of things on the island that hadn't happened yet. So it is feasible that people stayed behind to finish up there redemptions.
Just my interpretations. But something I have learned from this show, is don't assume anything, because 99% of the time you are completely WRONG!