There are dozens upon dozens of ways to fly in/out a logo. It can be done simply by using scale and position keyframes inside FCPX, or you can build an animation in Motion or After Effects. It can blur and fly, twist and fly, build like sand coming together or smoke becoming solid. It's hard unless you have an example of the kind of fly in you want to tell you how to get what you're looking for.
However, there are some things you should take into consideration.
Animating in a compositing program like Motion or AE is going to yield better quality results than animating in FCPX.
Animating a vector graphic will yield sharper results than a bitmapped image.
Is your logo 3D? Do you need to build it in a 3D program like Maya, Blender, or Cinema 4D?
Keyframing in FCPX can be troublesome because position keyframes are defaulted to an Ease in/out but Scale keyframes default to linear.
In addition to what has been said (all good advice), if you want to make a 2D logo into 3D and manipulate it in 3D space all from within Final Cut Pro X checkout my Boris Continuum Complete tutorials on Boris TV:
Extruded EPS Basics in FCP X, Part I
Extruded EPS Basics in FCP X, Part II
These tutorials will show you how easy it is to get some impressive results. People will think you used a motion graphics program like Apple Motion or After Effects but it's all done right in Final Cut Pro X with BCC 9. It's a great tool to have in your kit for work that requires motion graphics.