The small planes have roughly the same fuel consumption per passenger per mile as the large ones these days (AIUI the disadvantage of more engines balances the advantage of a larger plane. Maybe a hypothetical "twin-engine A380" could be more fuel-efficient - I'm not sure why that hasn't been attempted). So assuming equal loadings on all flights, point-to-point would be more fuel-efficient than a hub model (since passengers travel further in the hub model). Obviously if point-to-point leads to planes flying half-empty then at some point that becomes a bigger effect.