Clearly Travis Coates is the protagonist in Fred Gipson's novel Old Yeller. He is a fourteen-year-old boy who has been left in charge of the farm and his family (mother and little brother) while his father is away. Travis faces many challenges while he is acting as man of the house, and nearly all of them come from elements in nature. Because Travis (the protagonist) is in constant conflict with nature, nature must be considered the antagonist.
It is true that Old Yeller, a stray dog with an affinity for trouble, is often a source of grief for Travis. The dog not only does damage on the farm, but he is also a marauder, stealing from neighboring farms, as well. At times, however, the dog acts with Travis to save his family's life. Because he is not a relatively consistent opponent, though, Old Yeller cannot be the sole antagonist of the story.
Both wild animals and farm animals (certainly considered as part of nature) are in conflict with Travis often in this story. Dogs, bears, and more attack Travis and his family. Add to this the hydrophobia (a disease caused by nature), and even the Coates's own animals turn against him.
When his father returns and learns of everything that Travis endured while he was away, his father says:
"That was rough," he said. "That was as rough a thing as I ever heard tell of happening to a boy. And I'm mighty proud to learn how my boy stood up to it. You couldn't ask any more of a grown man."
Rather than any one person (though a possible case could be made for Mr. Searcy), it is the forces of nature which are constantly bombarding the young boy who is just trying to keep his farm running and his family safe. Nature is the antagonist.