Air is chaotic. It has unpredictable currents and areas of differing densities. Since planes rely on the comparative windspeed between the top and bottom surfaces of their wings to generate lift, these chaotic conditions cause lift to vary across the span of the wing causing vibrations and jolts.
Passenger planes can withstand an enormous amount of turbulence with no significant impact on safety. The seat belt signs are mostly to stop people from tripping over one another or banging their heads on the ceiling.
We hit a typhoon when I was flying back from Japan, the turbulence was bad enough that the plane would be in free fall for several seconds at a time. Everything was fine.
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