For one thing, D-II and lower sports are bare bones operations. Operating costs are minimal. No frills. Also, far less money is allocated for athletic scholarships (only 36 for D-II football compared to 85 for D-I). Many are on partial scholarships. D-III doesn't even offer athletic scholarships.
So, the answer to your question is that they don't generate much revenue, but they don't need to generate much revenue because operating costs bare bones. You ever watch the show "Last Chance U"? That gives you a good idea of what programs do to cut costs. Players dumping bags of ice in large kiddie pools and filling them with a garden hose to soak in. Players wash their own uniforms. Etc.
It's basically like comparing an MLB operation to a Class A operation.