Are you using Physics to launch the projectile or Transform.Translate?
Just as Lacju mentioned, spawn a projectile at a spawn point (Empty Game Object) that is a child of the ship, then translate, addForce or setVelocity in the "forward" direction the projectile. Just be sure to use "self space" and not "world space" when translating or adding force to the projectile if using a "forward" direction.
Alternatively, you can use the "Transform Direction" of the ship and use it to direct the projectile based on a vector3. Set the "Location Direction" Y:1 (if Y is "forward direction").
-ab