The island was reality, the rest was a purgatory of sorts (it explains why Locke was able to walk so quickly after his surgery). Jack died on the island as we saw him as a result of his wounds from the Locke/Smokie fight (he was not wearing the same suit he had been wearing when we very first saw him, so he did not die after the crash.
Meanwhile, I am guessing that Ben did not enter the church because he felt he never did really belong (his quote earlier in the season, "Because no one else will have me" rings true). I am guessing the same for Miles, Mr. Eko, Ana, Walt, Richard, Frank and the other flight passengers (and, if they had all died immediately in the crash, where WERE the other passengers, so again...island reality).