Whether and how the Indians benefited depends on who you talked to. The padres felt that by recruiting Indians to join the church and become part of the mission they were benefiting them by baptizing them in the Christian faith, and teaching them skills and the Spanish language.
The Indians who adjusted to mission life and many of the generation of Indians who were born at a mission might agree and some became very used to life at the mission. They liked being part of the community; they grew accustomed to the food and the ritual.
When the missions were secularized in 1832-33 some Indians continued to live at mission voluntarily. Other Indians missed the old ways where they were part of a small village and lived off the land, and didn't have as regimented and 'busy' a life. Some of these Indians ran away and this group probably didn't think there was much benefit at all.