My thoughts on "what happened" (spoilers)
The moment Alex character started saying "it doesn't matter what you do, because it all ends up the same, we'll all just disappear", it brought to my mind this philosophical theistic argument for morality: the existence of God is the basis for objective morals. Well, I'm not going to get into that any deeper, but this is a well known philosophical apologetic viewpoint. And it was made clear that Alex was an atheist who hated Christianity and the Bible.
Then I remembered that in the beginning of the movie there was John Denver's Rocky Mountain High played in the car of Jack and Tracy. Which is a Christian song in my opinion.
There was a little hint that Charlotte was a Christian. It was in the scene where Amelia held the Bible in her hands and fussed about the events being the retribution of God. Alex got really annoyed and said something like "I knew this was gonna happen, although I would have thought it would be Charlotte..." and then Charlotte gave him the middle finger. Charlotte was the only one who knew in advance the moment she'd disappear. She came to the bathroom door and said: "I'm going to go away now", the choice of words that also implicated that she was going somewhere and not just vanishing altogether...
Noah "falling in a ditch", which was weird as such, but in this Christian context of interpretation it would be a symbol of falling in sin and getting back up again. That's what it make me think anyway.
After all this I thought that maybe the disappearances were caused by an event called the rapture. It's a biblical interpretation that in the end times God will take His own people away from this fallen world.
But I came to a conclusion that it's not rapture that's going on in this movie, because everyone is taken, including insects and birds (and bodies of dead atheists lol). And there is this scene early in the movie where Sam is in the bathroom looking for Charlotte (the Christian woman) and he finds her shoes on the floor.
The rapture is in the Christian modern culture always pictured like that: those who God takes away from the fallen world leave behind pieces of clothing and shoes on the floor or in the street or shopping center or wherever they happen to be at the moment. But in the movie Charlotte comes to the bathroom in the next second saying she just went to get some paper towels. In my interpretation that scene was like a little hint that this wasn't a movie about the rapture, but that the events have more of a symbolical meaning...
All in all, to me this was a Christian film, or at least it had a so called Christian subtext. It was about the uncontrollability and shortness of the life on earth, unpredictability of one's death and the possibility that there's life beyond death.