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Airplanes flying through thunderstorms are often struck by lightning. According to a government site dedicated to the Centennial of Flight, during the '80s a NASA F-106B jet was purposefully flown into 1,400 thunderstorms and was struck by lightning over 700 times. Most commercial flights avoid the turbulent center of thunderstorms by flying over or around them. Perhaps more importantly, all commercial airplanes are outfitted with protective equipment. The shells of airplanes are generally made of either aluminum (an excellent conductor of electricity) or composite that contains conductive fibers so if the plane is struck, the lightning travels along the exterior of the plane then out into the open air.
Sensitive electrical equipment is shielded with surge protectors and grounding devices. The FAA tests every crucial piece of flying and landing equipment against lightning. According to this fascinating Lightning and Flight Quiz, on average every airplane in the United States is struck by lightning at least once a year. Lightning strikes have been implicated in only a handful of crashes worldwide. Lightning hasn't caused a U.S. airliner crash in about 40 years. Finally, this excellent article from Scientific American notes that airplanes often trigger lightning strikes when flying through a heavily charged cloud. When this happens, the lightning actually originates at the airplane and extends away in opposite directions.
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