This is an interesting question. Before World War II, commercial airline flights were extremely limited in space and had few black passengers -- because of the infrequency of occurrence, coupled with the awkward prospect of placing Jim Crow-style curtains or barriers in tiny, cramped planes that may or may not have had black passengers, state statutes never sought segregation on airlines. After WWII, commercial air travel in general increased, as did black passengers on flights.

The Civil Aeronautics Act of 1938 included a non-discrimination clause that prohibited unequal treatment based on a passenger's race. However, the "separate but equal doctrine" offered a convenient loophole for segregationists, who were able to claim that, by providing "equal" facilities to different races, nobody was receiving unfair or discriminatory treatment under the law. (It's generally regarded that many black facilities weren't actually "equal" at all, and actually much worse than their white counterparts, but that's for a different post.) While it seems like there is little evidence that commercial flights discriminated against African Americans, there are some exceptions. Ella Fitzgerald was famously denied her paid, first-class Pan Am seat on a flight from Honolulu to Sydney, Australia. She sued and won. I also found a newspaper clipping reporting that Chicago and Southern Airlines, Inc. asked black passengers to sit at the front of the plane on flights bound for segregated southern states. A Fair Employment Practices Committee examiner filed a complaint based on this discrimination, stating that he was "humiliated" by the policy, which perhaps indicates that such seat segregation was abnormal.

The big form of air travel segregation happened on the ground: terminals and other airport facilities in the South were often segregated. Unlike airlines themselves, these facilities were under municipal jurisdiction, not federal, and therefore not subject to CAA's non-discrimination clause. However, such establishments were highly contested; air travel's relative novelty meant that new airport terminals were being constructed well into the 50s that included segregated facilities, complete with "whites only" signs, during a decade in which the Civil Rights Movement was already underway. They seemed an anachronism to many. By July 1963, the last segregated airport (in Shreveport, LA), was forced to integrate via court order.

​

Sources:

Ortlepp, Anke. Jim Crow Terminals: The Desegregation of American Airports, University of Georgia Press, 2017.

Dixon, Robert G. "Civil Rights in Air Transportation and Government Initiative." Virginia Law Review 49, no. 2 (1963): 205-31.

Woods, Howard B. "Airlines Admit Jim Crow on Chicago Planes." The Chicago Defender, Mar 10, 1945.