In "The Open Boat" by Stephen Crane, in which the conflict is man vs. nature, what do the men fear about nature?

The men most fear their own death by Nature, that it does not particularly concern Nature whether they live or die because Nature is going about its own processes and practices. In the first paragraph, for example, the narrator says,

The horizon narrowed and widened, dipped and rose, and at all times its edge was jagged with waves that seemed thrust up in points like rocks.

Nature is brutal. It rocks and jostles the men in the boat with waves that are described as being as treacherous as rocks. The connotation of words like "jagged" and "thrust" is violent and harsh, and this illustrates the men's fear of Nature. It is uncontrollable, and despite their best efforts, they really cannot do much to help themselves. It feels, to them, as though they ride in a "bath-tub" because they are so dwarfed by the sheer enormity and awesomeness of Nature, of the sea, of the waves that are "most wrongfully and barbarously abrupt and tall."
By the end, the correspondent thinks,

Perhaps an individual must consider his own death to be the final act of Nature.

One's death really is just another fact of Nature, just another thing that Nature accomplishes, like trees growing or waves crashing. Finally, the arbitrariness of the oiler's death seems to confirm the validity of this thought and the men's fear. He is the youngest, is in the best shape, and has worked the hardest in the boat to keep everyone alive, and yet he is the one who dies "face downward" in the water.

The story is told mainly through the point of view of the correspondent, who is presumably writing about the experience after the event. What he and the other three men fear is mainly the indifference of nature. Nature cares nothing about them, whether they live or die. If they manage to get through the surf and to the shore, that will be a matter of sheer luck. If the boat is swamped by a big wave and they all drown at sea, that will also be a matter of luck. Nature is infinitely more powerful than these four men. 
The little boat, lifted by each towering sea, and splashed viciously by the crests, made progress that in the absence of sea-weed was not apparent to those in her. She seemed just a wee thing wallowing, miraculously, top-up, at the mercy of five oceans. Occasionally, a great spread of water, like white flames, swarmed into her.
Stephen Crane's main point seems to be that there is no god who has any compassion for human beings. They have to look out for themselves as best they can in this pitiless universe. Crane's short story "The Open Boat" makes the reader feel the imminence of death and the cold, indifference of nature. The boat itself seems to symbolize the fragility of human life.