I guess by RAW it would be so. If the target does fail the saving throw, is knocked prone even if flying, or without legs or anything.
Now, the consequences of the flying target getting knocked prone I don't know, I guess I would have a floating flyer use the "avoid falling damage" section of the fly skill, while I would resolve a winged flyer according to the "collision while flying" section of the same skill, but that's my interpretation...
