The following is a good discussion about turbulence in the air by U.S. Airways retired captain, John Cox (as seen in USA Today):
Question: Mr. Cox, can you please address the issue of turbulence, both in clear air and around thunderstorms? Also, related to flying near thunderstorm activity, what avionics and information do pilots use, beyond radar, to make route decisions. What is the general rule pilots use to avoid weather activity and therefore minimize turbulence for the passengers?
Answer: Turbulence is usually a change in direction or velocity in airflow (horizontally or vertically). This change causes a disruption in the smooth flow of air, similar to eddies in water. In clear air, turbulence can be caused by the jet stream, when high speed air interacts with lower speed air causing turbulent areas. Thunderstorms create turbulence by pulling large amounts of air in and sending it upwards very rapidly. Once this air cools, it has to come down, as it is heavier than the surrounding air. When it does, it can create microburst and very turbulent conditions. Pilots avoid thunderstorms by using weather radar which shows the precipitation within the storm. Newer generation radar can also show areas of turbulence. Each airline has specific guidance to pilots on minimum distances from storms.
Q: I am terrified of turbulence and of the plane going up and down and shaking. I have panic attacks every time the pilot turns on the fasten seat belt sign and once, he even told the flight attendants to sit down because we were encountering turbulence. When should I seriously start worrying about turbulence? Would the pilots ever tell us that something is wrong?
A: Turbulence is uncomfortable but very, very rarely poses a threat to the airplane. Designers and manufacturers take great care to ensure that the airplane can withstand very heavy turbulence. An example of this is the fact that injuries caused by turbulence are not uncommon, but the airplanes involved in such incidents almost never sustain damage.
Pilots avoid turbulence whenever we can. Reports from other pilots, relayed by air traffic control, allow time to climb or descend to the smoothest altitude. Occasionally, clear air turbulence is a surprise. That is when most turbulence injuries occur.
Asking the flight attendants to be seated is a precaution to keep them from getting hurt. One of the most common on the job injuries for flight attendants is from turbulence. No captain wants to take the chance of having a co-worker hurt on his or her flight.