Perks are special abilities and modifiers that every Class and Race grants at Level 1 and then every 5 Levels from Level 5 onward. For example, Worker evolving into Farm Hand: Worker would get perks at Levels 1,5,10,15,20 and Farm Hand would get perks at Levels 25,30, etc.
Most Perks provide a class with a new supernatural ability that usually scales with a Trait. For example: Line Cook has [If You Can't Stand the Heat] which provides Fire Resistance that scales with Constitution.
However, there are also some Perks that unlock new Traits by providing a single point in a Trait. If you didn't have that Trait already, then you can now spend Free Trait points on it. For example: Student has [Student of Magic] which provides 1 Magic Trait and makes it easier to study Magic Skills.
Jack has a unique Perk mechanic called General Perks. These perks don't come from Classes but rather were bought with Shiny Points during character generation. or from System granted Quests (potentially).