The atoms in milk move more quickly than the atoms in cereal, because liquids have faster atomic movement than solids, and the smashing of the milk atoms against the cereal atoms leads to diffusion. Diffusion is a scientific term for the breaking down of a solid.
Cereal initially floats on the milk because it has a lower density. As the milk diffuses into the cereal, the density of the cereal increases, which is why the soggy flakes make their way to the bottom of the bowl. Sugary cereals take longer to become soggy, because the milk has to work through the sugary film on the cereal before hitting the flakes themselves.