I provoke, but really, that is the question that burns beneath the beautiful surfaces of Terrence Malick's The Tree of Life.
I say this as an agnostic, as one who dislikes theology and theologians, but as one who (like many other critics) finds that this movie "touches me so much I can barely stand it."
The story opens with a title card displaying a quote from God. Job, a devout believer, has lost everything — his family, his fortune, and his health — and asks, in so many words: Oh Lord, why me?
In reply, the God of the Old Testament demands to know what right Job has to question him in any way.
"Where were you when I laid the foundations of the earth?"
It's a harsh response, but from God's perspective, a truthful one. (And to underline the point, Malick in the film takes the time to tell us the story of Job again, this time in a sermon. He has a minister in Waco Texas in the 1950's reminds his parishioners, including the family in the movie, of how instead of peace and kindness, God can "send flies to wounds.") Of how cruel God can be.
The human drama begins on a related note. The graceful, kind mother in the story, played by the ethereal Jessica Chastain, speaks in voice-over. As she speaks, we see her go from being a child, wrapped safely in the loving arms of her father, to being with the father of her sons:
There are two ways through life. The way of nature, and the way of grace. You have to choose which one to follow.
Grace doesn't try to please itself. It accepts being slighted, being forgotten. It accepts insults and injuries.
Nature wants to please itself, and for others to please it too. To have its own way. It finds reasons to be unhappy when all the world is shining around it. When love is smiling through everything.
As discussed in a previous post, it seems that this voice-over in the mother's voice is actually not what she is thinking, but what her oldest son Jack thinks that she believes. And yes, it does seem she believes in grace, and her husband believes in a Darwinian nature.
This sounds overly complex, no doubt, but in the context of the story it makes perfect sense. Jack, the oldest son, takes after his father, a stern controlling man, and not their mother, who loves them unconditonally. Jack grows up to be successful, but as he thinks back on the character, masterfully portrayed by Brad Pitt, he recalls a man who demands that his sons call him "Father," not "dad."
He thinks of how his dad tormented him, and how he in turn tormented his younger brother, a sensitive boy who takes after his mother, who refuses to fight — either his brother or his father — and who dies at age 19, of unknown causes, for no good reason.
Jack wonders if God the Father is as cruel as his own father, and his own self.
As the story develops, and as we see characters enveloped by trees countless times, we may well if nature is opposed to grace, or connected to it. (Jack's pain, and his mother's beliefs, may or may not be the director's.)
But there's little doubt but that this question of the cruelty of God is what Jack is wondering about, when he lights a candle in his grimly modern apartment in honor of his brother, and begins to think back on his father, his anger, his brother's death, and his own regrets.
We see it in the empty expression of Sean Pean, who is Jack as a grown man, successful, unhappily married, and alone. We see him yearning for the kindness and grace of his mother, and for forgiveness for them all. And as he looks back, questioning himself as much as his father, we see the harsh treatment meted out by his father paralleled by the harsh fate that struck down his younger brother.
How did she bear it? he wonders, thinking about the pain his mother felt over the loss of his younger brother. And as he mulls this, her words (in voice-over, in the past) begin to change: How did I lose you? (Is she speaking to God or his younger brother? Or to both? It's unclear.)
Who are we to you? Where are you? she asks God, the being she once trusted. The being she once believed lived in the sky, and pointed to in the clouds, assuring her infant son of his presence.
Universes of pixels have been spent on discussions of the twenty-minute genesis of life sequence in this film, which is as overwhelming as anything seen in 2001: A Space Odyssey. Many a complaint has been heard, that nothing in the drama of the not-especially-happy O'Brien family of Waco, Tex., in the l950's, deserves such grandeur. But that misses the point, the connection between the God the father to us all, and the father in this story, the father to Jack.
How can we love a father who is so cruel to us, and who insists on the goodness of his cruelty?

It's an enormous question, brilliantly dramatized (if left unanswered, in the end).
But what sticks with me are the last words of the mother, of the way of grace:
You can only be happy if you love. Unless you love, your life will flash by.