I think you need to consider a few things.
1. A good understanding of something's basic/fundamental properties doesn't mean that there isn't other more meaningful research to be done and knowledge to be gained.
2. Particle physics in general is considered a mess. There are still many open problems in particle physics and a shiny new accelerator never hurts ;)
Sure there is still a lot more to learn about the inner structure of protons/neutrons but that doesn't mean that we don't have a decent understanding of the overall picture. There still isn't one unified theory that explains all the natural forces, but that doesn't mean that we don't understand gravity/electromagnetism/strong/weak forces in their own right.