Jesus prays for three things in this passage: to be kept, to be sanctified, and to be sent.
Jesus did signs and miracles, and lots of teaching, however his primary mission was to reveal the Father. Before His arrest and cruxifixction He prepares His disciples (and by extension us) to go into the world and do what He did – reveal the Father to a world that is lost.
Jesus wants us to be close and connected to the Father. He wants us to be holy. He wants us prepared to go into a hostile world. So He spends time in prayer for us.