In Fallout, skills do not automatically improve through use. You can't raise them by spamming them. Instead, you are granted various quantities of experience points for the things you accomplish. You get experience points for killing things. You get experience points for finishing quests. You get experience points for assorted other things. Once you have accumulated a certain number of points, you gain a level.
Before Fallout 4, gaining a level earns you a certain number of skill points that you can distribute among your various skills as you see fit. Gaining levels also earns you perks.
In Fallout 4, it appears that gaining a level only earns you a perk. You can choose a perk that raises your level in a skill, or you can choose a perk that does something else. We have to wait for further word from Bethesda to know if this is really how things will work.