Yes, but Christopher Nolan is a singular artist making films on his own terms, and that includes the Batman trilogy he directed. With the Marvel films, there is a strict committee and house style to which directors must adhere. It isn't a place for auteurship, whereas Nolan's films undoubtedly are. That was Scorsese's point. He now thinks there are too many superhero movies and I agree. So does Christopher Nolan, by the way, who has ruled out making any more superhero films, frankly I suspect because he also thinks that.
All that said, I do disagree with Scorsese when he says Marvel movies "aren't cinema". In objective point of fact they are a work made for the cinema. In a sense, they are no different to the production line musicals, westerns, gangster films, and so forth of the classic Hollywood era. Most of them ranged from mediocre to utter rubbish and were forgotten. Today, it is the streaming platforms and their insatiable demand for "content" that is the reason there are so many artistically redundant films, television, and so on. Scorsese isn't wrong about that, but there's no point saying Marvel films aren't cinema.
One more thing: To be clear, I like Marvel movies. At their best they are first-rate entertainments, and I'd even argue Avengers: Endgame should have had a Best Picture nomination. Sometimes, the directorial prowess of those at the helm does shine through, even though they are not operating in uncompromised conditions like a Nolan. :)