All thunderstorms can produce severe turbulence, low level wind shear, low ceilings and visibilities, hail and lightning. Each of these hazards can be difficult to cope with; if all these conditions arrive at once, it can be disastrous.
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It's very unlikely for thunderstorms to bring planes down, and planes are able to be struck by lightning without suffering serious damages. In fact, rain, hail, and wind are more dangerous to planes than thunder and lightning.
When an aircraft experiences turbulence, the plane can drop or change altitude suddenly. This is why pilots always caution passengers to buckle up and stay seated when they are experiencing flight turbulence. The sudden movements put passengers at risk.