That the wind causes ocean waves is obvious to anyone who has spent time near the water, but the details of that process remain fuzzy. Many of the explanations — like the Kelvin-Helmholtz instability — only explain part of the process, usually the beginning when the waves are very small. As the waves get larger, they affect the wind in turn, complicating matters.
As messy as the theory gets, our ability to measure the wind and water in situ is limited, too. Just look at this wild research platform oceanographers designed to study wind and waves. It’s part of a 355-ft vessel that’s towed out to sea horizontally and then flipped so that 300 feet of it remain underwater to stabilize the remainder for measurements. Even with equipment like this, measuring the turbulent air and water near the ocean-sky interface is incredibly difficult.
This review article gives a nice overview of different historical efforts to explain how wind makes waves and provides a snapshot of the latest research in the area. (Image credit: R. Bilcliff; see also N. Pizzo et al.)