The adsorption of benzene on the Si(100) surface is studied theoretically using the self-consistent van der Waals density functional (vdW-DF) method. The adsorption energies of two competing adsorption structures, butterfly (BF) and tight-bridge (TB) structures, are calculated with several vdW-DFs at saturation coverage. Our results show that recently proposed vdW-DFs with high accuracy all prefer TB to BF, in accord with more accurate calculations based on exact exchange and correlation within the random phase approximation. Detailed analyses reveal the important roles played by the molecule-surface interaction and molecular deformation upon adsorption, and we suggest that their precise description is prerequisite for accurate prediction of the most stable adsorption structure of organic molecules on semiconductor surfaces.