If a player is launched by a wind charge, they of course do not take fall damage if they land any where above and including the Y-level from which they were launched. However, if the player is launched in the air, and then falls below that Y-level (for a distance from which they would assume fall damage) into a block which typically negates fall damage, they will take the fall damage after exiting that block.
To Reproduce (while in survival):
Stand on some sort of ledge, high enough that falling from it would apply fall damage, with water, or any other block which negates fall damage, at the bottom of the ledge.
Launch oneself from the ledge using a wind charge.
Land in the water/on the block.
Exit the water/block onto a solid block.
EDIT 1: This occured on one occasion after simply falling into water without using the wind charge, however it was just the one time. It occurs every time when using a wind charge.
EDIT 2: Includes all blocks or liquids which negate/reduce fall damage.
Can confirm. The report will have to be modified because it depends not only on water but also on everything that helps avoid fall injuries.
For example powder snow, sweet berries