The protagonist and antagonist may not be who you think they are. For one thing, a protagonist is not necessarily the hero of a story. Structurally speaking, the protagonist is the one who shakes up the status quo – that’s the “pro” part, while the antagonist is the one who tries to stop that effort or put it back the way it was.
In a James Bond film, for example, it is often the bad guy who begins an evil process that James Bond is called upon to thwart. This makes the bad guy the protagonist even though he is the villain, and James the antagonist even though he is the hero.
In practice, a true hero is a protagonist who is also the main character (we identify with him) and is also a good guy. A villain is an antagonist who is also the influence character (he has an opposing life philosophy or morality to that of the main character) and is also a bad guy.
But these traits can be mixed and matched between the two characters creating, for example, anti heroes and sympathetic villains.
The main point here is to stop thinking of protagonist and antagonist as hero and villain but as structural functions – to begin a quest or to try and stop a quest. Then, you can have some fun as an author determining which of these is the good guy and bad guy and with which one you wish your readers or audience to identify.