Why does rain make the waves on a lake calm out?
You are commenting on something that lakeside dwellers have described for a long time: Rain calms choppy waters. When waves are in progress, they are transferring energy horizontally through the water in an orderly fashion. The motions of water particles are organized and coordinated as waves move through, and the waves are moving in the same direction as the wind. More energy is added to existing waves by that wind.
When a raindrop strikes the surface of the water, it randomly creates a splash and then an eddy. Multiply this random effect by the millions of raindrops striking the surface of a lake during a heavy rainstorm and the addition of that random energy disrupts and dissipates the orderly wave train.