Sometimes the wind is gusty, and sometimes it moves in different directions in different places. When you’re in a plane, your wings are very good at catching gusts of wind, and you can quickly move from a region where air is moving up to one where air is moving down, and back into a region where air is moving up again. That’s what causes turbulence, and while there are dangerous things to fly in that cause turbulence, like thunderstorms, pilots are taught to not fly into them. There are many other things that cause turbulence without being a danger to the aircraft.
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