At the end of Fantastic Mr. Fox, why wasn’t the wife mad at Mr. Fox in the supermarket? Isn’t he again stealing?

I think you are partly correct, but there is more to it.

First, the climax of the film is not when the mine gets flooded. That's the low point of the film - the climax is when they rescue Kristofferson and escape the farmers. The flood does trigger him to change, but the nature of the climax shows that completely avoiding danger and not antagonising the farmers is not required.

Yes, Mr. Fox does need to change, as his wife tells him he must. This is in keeping with many of the patriarchal figures in Wes Anderson's other films. But that is not the complete message of the film. It repeats, almost ad nauseum, that they are "wild animals". Mr. Fox explains that "foxes traditionally like to...court danger."

There is a thesis-antithesis thing going on here, but by the end they reach a synthesis. They get to be wild animals, still stealing, but from the safety of the supermarket. Remember, Mrs. Fox did not object to stealing for moral reasons - she joins him in it at the start of the film - but because of the danger. The supermarket is a safe enough that she is happy to use it for food (what option does she have otherwise, anyway?) while he gets that thrill of messing with the farmers.

Mr. Fox learns to be content with what he can get; perhaps the apples are fake, but at least they have stars on them. Perhaps it's not as fun as stealing from the farms directly, but at least it's stealing from the farmers.