Everything that happened on the island happened. It was all real. The flash sideways was when they were all dead. They all died at different times, some before Jack, some after him, like Christian said but in the afterlife there is no timeline so they were all there together. The flash sideways was like a resolving of all their conflicts and inward strife. Jack became a better father, and was able to make peace with his father. Claire decided to keep her baby, and was reunited with her family. Kate was finally able to help someone else, Sawyer was a cop, not a con, Sun and Jin were together and happy, Sayid found Shannon again, Charlie was alive, Locke reunited with Helen and regained use of his legs, etc etc. To paraphrase words of C.S Lewis from the wonderful book The Last Battle, "all things sad became untrue." In my opinion, the flash sideways was a picture of redemption for all these sad, broken, and flawed characters that we were introduced to 6 years ago.
They were in this flash sideways together until each one of them was ready to let go and move on. One major theme of Jack's character that we saw over and over again through these 6 seasons is that he had a hard time letting go (remember the episode with Boone?). That's why he was the last to arrive. It's also why Ben's character didn't go in. He wasn't ready yet. He still had things he had to work out. Very fitting, in my opinion. I think they were all in the church to move on to the next stage of afterlife, ie, heaven, together. As my brother Andrew put it, very much like Frodo and Gandalf setting off to the Grey Havens. Maybe it's not theologically correct, but I think it's beautiful. Again, it's also very Last Battleish; all of the characters walked through the barn door at different times, and died at different times, but they ended up together(dead) in that limbo land waiting for Aslan to arrive.
No, all our questions were not answered, and it may have even left us with more questions.... but isn't that part of the beauty of the show? Some things we just have to accept as being part of the island's mystery (like why women can't carry to term).
I think every religion can probably take something from the show, but I definitely see a lot of Christian and Gospel parallels in the season, and especially in the finale. The most obvious, of course, is Jack's sacrificial death in order to save the lives of his friends. As my dad put it, "the good shepherd laid down his life for his people." I have no idea if the writers meant for it to be interpreted this way. They probably didn't, but even Hollywood can't help but reflect the power of the gospel. It is embedded into every great story, because there is nothing more moving or more powerful than someone's sacrificial death to save others.
Another thing to ponder: Jacob is like Adam. The one thing his "mother" forbade him to do was to go into that light, but he screwed that up. Through one man darkness (black smoke) entered the island, and through one man, darkness was defeated and light was restored.
Man, I love this show and I'm so gonna miss it!