The boat in Stephen Crane's short story "The Open Boat" represents man's attempt to overcome nature.
Crane was a Naturalistic writer. The Naturalists were authors who looked at their texts as observations made from a scientific perspective. They, the authors, were simply observers and did not "interfere" with the action of the story.
That being said, nature was the most powerful entity on earth. Nature had all of the power, man had none. Whenever man and nature would come together in an external conflict, nature would always win.
Therefore, the boat (what "protected" the men from nature (the ocean)) represented man's attempt at rising over nature. The boat was the only thing which was protecting the men from being in the water (an element of nature).