They don't get together, but I think that's the beauty of it. On one side, you have the main love story, which is saccharine but cute, and on the other hand, as a balance, you have the Soujiro-Yuuki story. I'll paraphrase what someone else here has said. He runs away because he KNOWS he'll fall for her, [and to add my own part] but he's convinced she'll get hurt. :)