Whether its inspiration for this movie is The Fetterman Massacre of 1866 or Custer's Last Stand in 1876 doesn't really matter. What does matter is that this is a great movie. It is the first in a cavalry trilogy for John Ford (She Wore a Yellow Ribbon, Rio Grande), I think this one is the best.
In the movie Colonel Thursday has been assigned to command an outpost where it doesn't seem likely that he will be able to gather glory and further his career.
Thursday doesn't think much of the "digger Indians" that are in this part of the country. Captain York, played by John Wayne, informs him about how formidable the Apaches are but Col. Thursday is doubtful.
The movie is one of the first to give a positive portrayal to Native Americans. Cochise is portrayed as a proud, intelligent and merciful leader. He clearly outclasses Col. Thursday in all areas. He is forced to defend his land. When he has the chance to massacre the survivors of the battle, he does not.
One of the most interesting aspects of the movie is that even though Col. Thursday is an arrogant, ignorant leader he still goes down in history as a heroic commander. I think this is Ford's statement on the "American" history of the West. History is often written by the winners and that point is driven home here. Fort Apache makes a very early statement about the need for an American history from the Native American point of view.
In his wonderful book, Gunfighter Nation (1992), Richard Stotkin says of Fort Apache: "But in Fort Apache the meanings of the symbols is inverted: the colonel of the regiment is a fanatic and tyrant who breaks the code of warrior honor, women's values stand equals to men, the Indian's are victims and honorable fighters rather than savage rebels or aggressors, and the film's last stand is less a glorification of Western civilization than the culmination of a subtle critique of American democratic pretenses." Of the ending of the movie Slotnik observes of John Ford's movie that "it also provides us the the mythic basis for a new ideology, designed to build national solidarity in the face of the threatening advance of Soviet Communism - an ideology which (if Ford is a true prophet) would ultimately rest on a deliberate and consensual falsification of history."
Slotkin is pointing out that while Ford is criticizing American's treatment of the Indians, he also understands the importance of putting a better spin on our history, so that we could create a common mythology and belief system that would help us in the upcoming fight against the communist menace. So in effect, the poor treatment that Indians received at the hands of the Whites, should be covered up in the name of patriotism and myth making.