Every story must have at least one protagonist (that's the character you cheer for) and one antagonist (the thorn in the protagonist's side). The antagonist need not be a person. It could be an obstacle like a traffic jam, a natural problem such as a tornado or wild animal, or even simply an internal struggle (should our hero keep the money he found or turn it in?).
We readers always cheer for the protagonist, but our feelings toward the antagonist aren't quite as clear cut. If a raging river has our hero fighting for his life, of course we want him to win the battle, but we don't really bear any grudge against the river. It's just doing what rivers do. It is posing a problem for sure, but it is not something for the reader to despise.
With human antagonists, it's different though. They tend not only to be obstacles; they become villains. The river is destined to overflow its banks -- it can't help itself, but human antagonists have choices, and when they choose to make our hero's life miserable or dangerous, we get a full-out hate on for them.
The thing is no protagonist is all good and no antagonist is all bad. Unless the goal is cliche characters like Simon LeGree (Uncle Tom's Cabin) and Prince Charming (Cinderella), a writer needs to mix things up, so that the bad guy has one or two redeeming qualities and the good guy has a couple of flaws. Sometimes the faults and strengths can seem so even in the hero and villain that the only way we're really sure who's who is by which character overcomes his flaws and which gives in to them. Case in point would be Obi Wan Kenobi and Anakin Skywalker in Star Wars. They were master and student and best of friends. We loved them both. But when Anakin gave in to the Dark Side of the Force, he became Darth Vader and his role as villain was set in stone. We still liked Anakin, but it was as if Darth Vader had killed him. (You see how George Lucas did that? We writers are tricky.)
I've always thought it would be an interesting exercise to rewrite a story from the antagonist's point of view, wherein he/she becomes the protagonist and the plot now sheds a positive light on his/her actions to see if readers who formerly despised him/her might have a change of heart. Kids do it all the time when recounting a misunderstanding (black eye) or mishap (broken lamp) to an adult authority. Two children = two stories = two heroes & two bad guys. If kids can make an argument for both sides, a writer should be able to too -- right?