The protagonist is a story's main character. They are present for all the most important events in the plot from beginning to end, and they are usually meant to be sympathetic and identifiable with the reader. Their opposite number is the antagonist, who works against them and their goals. There can be multiple protagonists in a story.
It is important to note that the protagonist is not necessarily a hero. It is possible to have a protagonist with whom the readers sympathize despite their questionable actions, desires, ethics, and/or morals (known as an anti-hero), and it is possible to have a deliberately unsympathetic protagonist, though this is difficult to pull off.
A good example of the former is Dr. Horrible of Dr. Horrible's Sing-Along Blog: while technically a villain whose goals include world domination, he's also a bit of a dork who has trouble talking to a girl he likes, and his "hero" antagonist, Captain Hammer, is a complete tool.
An example of an unsympathetic protagonist is Thomas Covenant of The Chronicles of Thomas Covenant the Unbeliever, who spends most of his time being a selfish jerk who refuses to step up and own his power to save the world, despite everyone else in the series politely insisting that he can and must. He is propelled unwillingly through the story by side-characters who are, fortunately, much more likeable than he is.
The protagonist may or may not be the viewpoint character.