I think the central preoccupation is what we do when we discover that people are not perfect, that they may not live up to our expectations of them. We actually do not know what happened in the woods, and are left to suspect that nothing may have happened and that it might have been a dream. The fact that we do know is that the Brown who leaves the woods can no longer look at his townsfolks with the same acceptance as he once did; in fact, he becomes isolated from his wife, Faith, and his faith in the goodness of the townfolk, and this leads him to live a miserable life and die an unhappy man.
Stated briefly, Hawthorne's central preoccupation is with accepting the ambiguity that is part of life; there is good and bad in everyone and everything and we have to accept it or be as miserable as Brown.
There seem to be a number of central oppositions that are explored by Hawthorne in this short story. Good vs evil is an obvious central theme. Some aspects of this story can be viewed as allegorical, and certainly the trip into the forest seems to assume a greater significance than just a trip. The fact that Brown only has to do it once suggests that this might be viewed as a spiritual quest that all humans have to undergo at somepoint in their lives: an exposure to evil. However, Brown is unable to live with the truth of humanity's fallen nature. Faith, his wife, on the other hand, is able to welcome Brown back with open arms. There is a contrast then between his reaction and her reaction: Brown's absolutism and the absolutism within Puritanism at large is shown to be a moral cancer that saps the joy out of life and leaves nothing but suspicion and distrust.