The protagonist is the one we root for in the novel—the character whose life we're most concerned with or whose inner life we're given access to. A protagonist is often opposed by an antagonist of some sort, who keeps our main character in conflict until he triumphs over it. Or not.
A protagonist doesn't always wear a white hat, and he doesn't always fight a dude wearing a black one. The best protagonists are often the most complex—sometimes kind, sometimes loathsome, always engaging.
Shmoop's personal favorite? Yossarian, hands down.