not sure what you are asking, but shuttles are used for shuttle content. Missions where a starship can't be used. You can get shuttles with a requisition when the mission comes up or for something better than the "stock" version you can pick up different ones (including fighters) from the Zen Store or by spending Lobi Crystals. If memory serves, there are three missions involving shuttles thus far including one that is located in the PVE queue.
Shuttles are part of a "small ships" class, along with fighters and some support ships. They are basically smaller versions of the starships, with the same weapons and equipment as the bigger ships, but with fewer slots.
You can use a small ship as your pirmary ship if you want to, although you wont live very long in most of them. There are, however, a couple of missions that require you to use them.
You will be given the simple shuttle for free if you want it, but can buy a different small ship if you want to. The runabout is pretty cheap, and is much more robust than the basic shuttle. They also sell some for zen on the store site. Same as the other ship classes, some are free, some are in-game money, some are rl money, use what you want.