As a penalty... well, the motorcycle will most likely not have any natural attacks.
The pros... Well, It's freaking cool, for one. You have to pay for gas and repairs, but overall it's much easier to care for a bike than a living thing. They are also faster and don't get tired. If the player wants a tangible benefit for giving up her mount' natural attacks, then I suggest increasing its speed by +10'.
I recently created a home built Starship Pilot class for a Sci-Fi PF game based on the EN Publishing Santiago setting rules, using "ranger" as a template, though its not intended to be a ranger archetype, rather its own base class. As a part of this build, I created the Pilot ability which is five levels of vehicle training, with Pilot 1 allowing driver skills use of automobiles, motorcycles, hovercraft, submersibles, aerial vehicles, escape pods and orbiting shuttles. Pilot 5 at 19th level allows a starship pilot to manage an interstellar fleet. This doesn't fit your premise of a vehicle for a cavalier class, however.
I would certainly allow a sci-fi based "cavalier" to be able to operate an automobile, motorcycle, hovercraft (including a hoverbike), submersible, aerial vehicle, etc. The ride skill would be of obvious use to perform difficult driving maneuvers, though I don't know if there'd be a reason to replace "handle animal" with something else.
I see, but could you post a link to the santiago far future download? I downloaded it before but it seems there have been some updates since my last download.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.