Clear Airm turbulence can have many causes, but among the most common are rotors and air pockets. The atmosphere is a dynamic system, and the pressure within it varies according to the temperature of the air. If air is warmed it expands, leading to an area of decreased density, which rises. This air will provide less lift than more compact air. A plane flying through these "air pockets" tends to experience that horrible dropping like a stone phenomenon so beloved of travellers. Rotors can be left behind by other aircraft, or by mountain peaks. These are effectively whirlwinds on their sides, swirling horizontally, and can give you a very bumpy ride.
The short answer is that the bumpiness you feel on a plane is due to unevenness or motion in the air supporting it.