The protagonist of story or novel is the hero -- the person we are rooting for or that is the focal point of the story. Sometimes they can be horrible people, but in this case, the protagonist is Harry Potter. He is the very special boy who is finally learning the truth about his talents and his place in the world -- a wizarding world he knew nothing of until now.
The antagonsist(s) of a story or novel are the characters who create the conflicts for the protagonists. There are several characters who fit this bill in the novel.
The most obvious, and prevasive, is Voldemart who is determined to take over the magical world with his evil ways. He must destroy Harry in order to do it, and while Harry likes Hogwarts school and his new friends, he doesn't know whom to trust.
Other antagonists in this novel: The Dursley's -- Harry's aunt and uncle who are his guardians, but who treat him very poorly; Draco Malfoy -- the bully from Slytherin; Professor Snape whom Harry and the other kids think is trying to hurt Harry (though in the end it is revealed that he was protecting Harry); Professor Quirrel, it is revealed, is the true "bad guy" of the novel as he is the working working for Voldemort and who wanted the Sorcerer's Stone.
The protagonist of a story is the story's main character, which, just as the title suggests, is Harry Potter. The antagonist is the person who works against the protagonist in the main conflict of the story. Although the antagonist does not necessarily have to be "the bad guy", in the case of Harry Potter this standard "bad guy" image continues. In the series as a whole, the antagonist is Lord Voldemort as Harry continuously comes into touch with Voldemort while trying to save the Wizarding World. However, for the first book alone, the antagonist could just as easily be Quirrell. As he shares a body with Voldemort, it is difficult to separate the two characters when discussing who the antagonist is. The qualities of the antagonist were the intentions of Voldemort carried through by the actions of Quirrell.
In a broad sense, the protagonist is Harry and the antagonist is Voldemort. However, Harry doesn't really come into contact with Voldemort until the very end. He doesn't even realize it is Voldemort until the very end. So its tempting to say that Quirrel is the antagonist. Yet, "no one suspects poor stuttering Professor Quirrel". Harry suspects Snape throughout the whole novel but it wasn't Snape!