A player's alignment usually refers to the faction with whom the player shares the same Win Conditions.
Most players in the average game will be Town, and the town could be called the protagonist of the game. These players usually will only know their own alignment and role (with the exception on masons). The town is also used to collectively refer to all the players in the game. A default town with no role is referred to as vanilla town. The town will usually win when no threats to the town remain alive.
The Mafia is the antagonist of the game, who tries to win by staying alive and killing enough townies to control the vote (when they are 50% or more of the town). The basic mafia role is referred to as a goon.
Other players in the game can be separate from both the town and mafia entirely, and have their own win condition to fulfill. They usually are anti-town in that they don't have to kill the mafia to win, and may not be helpful in that endeavor. Survivors, Serial Killers, Jesters, and Lynchers are all examples of third party roles.