Most of the time, the protagonist and the antagonist of a story are easily identifiable. In Shakespeare's "Othello", Othello is the protagonist who tries to resist killing his wife in a jealous rage, and Iago is the antagonist who pushes Othello to the breaking point. But in other stories, the protagonist may be an imperfect character or anti-hero. He or she may be doing the right things, but not entirely for the right reasons.
Another character may be a reluctant antagonist. He or she doesn't intend to cause trouble or work against the protagonist, but that's how the circumstances play out. A desperate scientist may try to create a cure for his dying son, which would make him the protagonist. The director of the lab may do everything to keep him out of the lab, which would make him the antagonist. In reality, however, both men would be acting out of good and bad intentions. It isn't always easy to sympathize with a protagonist or despise an antagonist.