The two key parameters dictating transport across molecular junctions are the barrier height and degree of coupling between the molecule and leads. Stable molecular junctions require chemical binding to the substrate, which often interferes with the net transport across the junction. Si offers various stable binding chemistries, such as Si-C, Si-O or Si-N, leading to uniform, high-quality monolayers. This allows a systematic study on the role of the binding group and linker to the aromatic core on the electronic structure of the junction. Combining ultraviolet photoelectron spectroscopy (UPS) and density functional theory (DFT), we have studied the electronic structure of aromatic self-assembled monolayers, covalently bound to Si, using several different aromatic groups (phenyl, biphenyl, and fluorene) and binding groups (O, NH, and CH2). We obtain excellent agreement between theory and experiment, which allows for a detailed interpretation of the experimental results. Our analysis reveals a significant effect of the binding group on state hybridization at the organic/inorganic interface. Specifically, it highlights that lone-pair electrons in the binding atom facilitate hybridization between the aromatic system and the Si substrate, resulting in a significant induced density of interface states (IDIS). These interface states are manifested as a broadened HOMO peak in the experimental UPS data and are clearly observed in a theoretical spatially-resolved density of states map. Our results provide the understanding and insight that is required to tune the degree of coupling between substrate and molecule, which is a key factor controlling the net transport across molecular junctions.