First off, he was doing independent films for a significant chunk of his career. Because of that he did not have the studio system to promote and distribute his films, so he was facing significant headwinds even getting his films into theaters.
Second, he did not make movies to make money – so he rarely made films that were targeted at popular audiences. An adaptation of Kafka’s The Trial or making a film about Falstaff are not choices a “hitmaker” would make. He wanted to tell stories he personally felt connection to, and he was a man of very distinct tastes not shared by all.
Finally, many of his later movies are very “distant” in the way they are shot – he did not do some of the tricks that many directors do to increase audience empathy and engagement. For an example, look at how Spielberg uses shot composition, music and editing to bring you INTO his films. Orson had his own style which was… not that. He still was an amazing filmmaker, but the style was not one that made Joe Six-Pack rave about his films.