[arrowheadnation]

This is the best explanation I've seen...

We all have our mixed opinions now on what the island was, is and what this ending was about. The island was real. Yes Jack died right then and there on the ground in the bamboo next to Vincent. And Ben, Hurley and the rest of the Losties that remained on the island, stayed there until they passed hence Ben and Hurley calling each other good #1’s and #2’s. And Kate, Sawyer and the Losties that left the island on the plane lived out their lives until they died (or perhaps the plane didn’t make it and they died in a crash...only Damon and Carlton know). The alternate timeline was purgatory and the church was the pearly gates. When you die, time ceases to exist. Everyone in the alternate timeline died at some point. It does not matter when, because time is not a factor. Time is a concept made up by human beings. When you die, not only will you be in an afterlife with your ancestors, but also your children, your grandchildren, even your great-great-great-great-great grandchildren. As soon as you die time ceases to exist. This was the biggest event in each one of their lives and it meant so much to them so God wanted them to enter Heaven together as one.

To elaborate a little more (in my own words)...

In heaven, the great beyond, the next life, however your religion may perceive it, there is no such thing as time. LOST was basically the story of how Jack Shepard got to this great beyond. If it would have been the story of how Shannon got to the afterlife, we would have saw her story up to her getting shot, then we would have seen her arrival at the church with everybody (including Jack) already being there. If it would have been the story of Sawyer, we would have saw all the events up to him dying as an old man, getting hit by a bus, having a heart attack on the mainland. And in the alternate timeline, he would then show up at the church.....and of course everyone would already be there. You just have to tell your mind to let go of events happening in a certain order or timeline.