A 50% capacity factor does not mean there's no wind 50% of the time. It only means that, averaged over a whole year, the power produced is 50% of the maximum the generator is rated to produce. This includes periods of time when there's wind, but wind that's not strong enough to reach the maximum output of the generator.
And the wind not being strong enough to reach the maximum output of the generator is probably the most common situation, since it makes sense to design the generator to reach its maximum output at the strongest normal wind on the region; when the wind is stronger than that maximum, the generator has to shut down (feather the blades and brake the rotor), otherwise it will get damaged.