Great question! Of course, when we think about the symbolic meanings of acts like the one you referred to, it is often not spelled out directly in the text, but there is enough evidence to infer the meaning. Certainly one meaning is given for us when the father shows the flare gun to his sun and says they will fire it:
We can shoot it.
In the dark?
Yes. In the dark.
It could be like a celebration.
The boy himself labels the act of firing the gun with a celebration, presumably to celebrate their safe arrival at the coast.
The actual description of the firing of the flare gun leads me to think that it is also symbolic of hope:
The flare arced up into the murk with a long whoosh and broke somewhere out over the water in a clouded light and hung there. The hot tendrils of magnesium drifted slowly down the dark and the pale foreshore tide started in the glare and slowly faded.
The flare managed to penetrate the "murk" of the sky, symbolic of the state of the world, and still gives light. This to me is symbolic of the hope that the boy has that there is a chance of survival and there are some "good guys" out there to help him.
Lastly, the firing of the flare gun could be said to represent a memory of what times were like before and the limitations of humanity. Interestingly, after seeing the flare, the boy says:
They couldn't see it very far, could they, Papa?
This could be read as a recognition of the limitations of humanity and how they created the mess that the boy and the father are trying to survive in.