It's an interesting film because it really lacks a plot. It displays the existential struggle of mankind in raw form, inviting you to make your own life the plot by revealing it in visceral representation. It raises many questions and makes few statements, but the statements it does make are beautiful.
It is important to see the narrative overlays with the different sections. Obviously throughout you have the nature vs grace concept, and especially represented in the mother and father, but there are others. The progression of life on earth and mass extinction is correlated with the progression of a single life. The questions raised by the rise and suffering of life are reflected in the rise and suffering of self awareness. The drive and failure to succeed in fatherhood is correlated with the natural creation and drive unto life which is all made futile in natural death. Yet the victory of the aspects of grace over the destructive natural drives by the manifestation of forgiveness is seen as a promise that grace also in some way has victory over the natural death, even that of the whole earth eventually.
It's hard to remember all the exact signals, but there is stuff like the buzzing and bells tolling which indicate passing of life, and perhaps arguably the school bells marking the passing of innocence. The washing over of water is also as a mark of death, in the case of the pool scene perhaps the death of faith. Yet rising from the water is also shown as the beginning of life, most obviously shown as the child rising out of a house underwater cutting to the mother giving birth. Yet the rising of the natural self is also shown as being hindered, shown by hinted entanglement in the plants underwater at the same time of moral entanglements. The music is an example of discipline manifest into beauty, a representation of the original dream of the father/natural creation and drives.
Moving away is a sign of accepting the failures of the natural in recognizing its true meaning, also reflected in everyone's attitudes, yet the destination is left mysterious. This is doubled over by the themes of the passing of a life and ones own life. The area where they go to meet the end is the same as where life itself was shown to begin. The brother is led there by his younger self, which says that his own journey of self awareness and moral development was guiding him to understand where he will go at the end. In that place the origins and intentions, the purposes and manifestations, the resolutions and hopes all meet together, so it has multiple generations shown in the same spot, and multiple representations of the same person.
Looking at that, I think with the mother accepting the passing of her son in trust, she has another woman behind her and a young girl in front of her. I think the other woman is what her mother was like when she was a child, and the child is her younger self. She is taking a similar journey that the brother just had, except instead of existentially questioning oneself, she is using it all to have hope that the life and death of her son was for ultimate good. Being the representation of grace, and her embracing the whole family and the younger and grown son at the end, a view to their unity in collective existence and fate, is why I think it is taken as a promise.
There is also a lot said in the fact of a brother dying and the nature of brotherhood, and looking at them at representations of the brotherhood of mankind in general, and looking at the parents not just as premises of existential questioning, but the facts of history of mankind, the traditions and philosophies that went into making us what we are, and how a look to our younger selves and the lessons we learned in the "childhood" of humanity may be a guide to seeing what overcomes all we wrestle with, and what guides us to find the unity of all that wrestles within us and hope in full view of our inescapable fate, which is made so visible by the death of innocents among us, especially in war.
Being a Malick film, I'm certain there is a lot more to be found in multiple viewings. And, like all his films, in one sense you may be uncertain how to feel, because there is no fully clear intention or direction behind all of its insights, so there can be no immediate satisfaction that it wrapped up every proposition it made. However, I think if you consider all the films you have viewed in your life, you will find very few have been so penetrating, insightful, and intimately familiar with and representative of the core of human experience. Some of those few may be other Malick films. For this, I can offer nothing but praise.