Stephen Crane's very short but pithy poem "A Man Said to the Universe" is an expression of its author's generally bleak view of man's relation to the cosmos. One has only to read some of Crane's other work such as his short story "The Open Boat" to see further examples of this grim, uncompromising attitude. Here, as elsewhere, Crane is at pains to emphasis the relative insignificance of humankind in the overall scheme of things.
From our human-centered perspective here on earth, we are at the center of the created order. It is this attitude which gives us the confidence—indeed, one might say, the arrogance—to affirm our importance in relation to the universe. That is what the man in the poem is doing when he proudly affirms to the universe that he exists. He is respectful towards the universe in that he addresses it as "Sir". But there is still more than a hint of pride in what the man says and how he says it.
But the universe's withering response puts man's existence into a completely different perspective. Yes, the universe acknowledges man's existence, but that doesn't mean that it has any obligation towards him or his welfare.
On this reading, the universe is utterly indifferent to man's wellbeing. It doesn't act as a kind of benevolent deity, constantly involving itself in man's affairs and regularly intervening to protect him from danger. On the contrary—from the standpoint of eternity, which is the perspective enjoyed by the universe, mankind is of no great importance. Yes, he exists, but so what?