Sean Penn is a Houston architect in a world of steel and glass. News of a family tragedy shakes his foundation. He is forced to remember that humans design awesome structures but have little control over the cosmos in which we set them. The Tree of Life begins with a quote from the Jewish scriptures about God asking tragedy-struck Job, "Where were you when I laid the earth's foundation?"
The architect comes to realize he is not THE Architect. He wonders "Why am I here?" and "Where am I going?" plus "Is the ultimate force behind the universe embracing of my value like Mom or demanding of my submission like Dad. The answer: bit of both. You may not like Malick's conclusions or his imagery in framing the questions. However, if you're waiting for Hollywood to make a more sincere philosophical reflection in your lifetime, don't hold your breath.