With all respect to the previous two editors, perhaps one can say that "A & P" has no real "message," but is rather an insightful sketch of teenage attitudes and behaviors.
The girls seem unaware of the social norms that they are violating; the boy is moved to an impulsive, self-destructive act by force of his confused sexual yearnings; throw all this together with the boy's rebellion against his parents' middle-class values of working hard and keeping your mouth shut, and you've got a perfect picture of a typical bunch of teenagers.
Now, I don't mean that there really is no message. I do mean that there is much to learn from this story without searching for a "moral."
In John Updike's "A & P" there does not seem to be any apparent indication that Updike sends a message to the reader that "it is good to be yourself." For, Sammy's act is quixotically romantic as he gains nothing from it; instead he loses his job. Because of this action, there have been varying interpretations of this story. Some argue that Sammy rebels against the disparagement of the girls by the Puritanical management while others contend that he quits because of misguided interest in the girls, thinking his act chivalric.
At any rate, there can be two themes that emerge from Updike's story: Individual vs. the Collective, and Conservatism vs. Liberalism. With both of these the message may be that sometimes there is a split between one's inner feelings and society's values.
In my opinion, the message of this story is that it is important to be yourself, but you have to realize that being yourself has consequences in the real world.
I think that the story is about individualism. The girls (or at least Queenie) are expressing themselves by the way they are dressed. Sammy wants to express himself by defying his boss and by acting out against the social values and conventions that his boss is personifying. To the extent that he makes the girls and Sammy sympathetic, Updike seems to be telling us that it is good to be yourself.
But the message is mixed some. Neither Sammy nor the girls comes out of this 100% happy. Both are punished in some way for choosing to be individualistic. This says to me that part of the message is that we may have to pay the price for choosing to go against society.