A handful of jets have been blown up by lightning, including a Pan American flight in 1963 that killed 83 people.
But scientists have since figured out how to mostly harness Nature's fury. In the early 1980s, NASA (whose shuttle launch pad was struck by lightning the other day) flew a jet into a thunderstorm at 38,000 feet. It was hit 72 times in 45 minutes, and much was learned.
Commerical planes are still hit about once a year, by some estimates. A strike typically starts at a wingtip, nose or tail and courses through the skin, which is often made of aluminum—a good conductor. The plane's lights might flicker, but most of the energy just heads back into the sky if there are no gaps in the skin.
Modern jets often employ advanced composite materials, which are not so conductive, so metal has to be added to the composites to carry the lightning.