First, remember that the airlines and the FAA have teams of meteorologists working to predict the weather and, if they see some bad thunderstorms building up and the economics justify it, they typically choose more favorable routes of flight to avoid the severe storm potential altogether. What if the economics don't justify it and they can't be avoided? Remember - crashes are really expensive for the airlines. You'll be sitting in the terminal yelling at the gate agent. But, as we all know, on a warm, humid summer day, stuff pops up and planes still fly so, how do they get around it? The answer is: very carefully.
First, every airliner is required to have onboard weather radar. In the nose of the plane, there is a little radar dish that the pilots aim at various points of the sky to measure how much water vapor is in the air. The more water they see, the greater the chance that it is part of a severe storm. The pilots use this radar to calculate which route will keep them away from the storms. They then request that deviation from their assigned route to Air Traffic Control (ATC) and 99 out of 100 times, ATC approves the deviation without question. What happens when ATC doesn't approve the deviation? Well, the pilots do whatever they need to in order to keep your flight safe. Just because a guy sitting comfortably in a radar room tells your pilots they need to fly though a thunderstorm for traffic spacing doesn't mean that the pilots are actually going to do it. After all, they are the "Pilot in Command" and are the final authority on the safe operation of the flight....sorry God, it's right there in the regulations....the pilots are the final authority.
What about low level wind shear (LLWS) and other wind shear? Well, ever since the Delta L-1011 crash that I mentioned in my last post, the FAA mandated that every turbine powered passenger aircraft (basically everything you fly in with a jet engine) must have wind shear detection onboard. Thru a NASA developed technology known as PFM (or Pure Friggin' Magic), a computer analyzes the onboard weather radar to calculate whether or not wind shear exists. When your pilots hear the plane yell "WIND SHEAR! WIND SHEAR!" they get out of Dodge (or Cleveland as the case may be) quickly.
The airplane is not the only way LLWS is detected. Most airports that the airlines fly into have wind shear detection sensors all around the airport. Wind shear, by definition, is when you have wind going in many different directions. So, when those airport sensors start detecting wind going in a bunch of different directions in different locations around the airport, they alert ATC so they know that wind shear has the potential to exist at the airport when planes are in their most vulnerable condition: low and slow. ATC will in turn notify your pilots and your pilots will react and fly the plane as the conditions dictate.
So, the next time your flight is delayed because a huge thunderstorm is rolling thru the airport, head to the bar, grab drink and lay off the gate agent. Trust me, you'd rather have a Guinness in your hand than a thunderstorm.
EDIT: Douglas makes an excellent point in the comments below. ATC has weather radar as well that they use to coordinate deviations with the pilots. In fact, if you hear some storms rolling thru your area, go to LiveATC.net and find a local airport feed to listen to. It is amazing to hear the professionalism of both pilots and controllers as they safely navigate planes around storms. Thanks Douglas!