I thought they made perfect sense (Seven and Chakotay) because he was a bit of a teacher to her and brought out her humanity more. She came to appreciate his view of things, his anthropological view like in One Small Step and the one where they crash. They were almost opposites, but there was a bit of teacher/student going on there and it was clear that admiration developed. Seven was more like a young student at college, so I can see how that would appeal to Chakotay and how his views would appeal to her. He pushed her to see things but not to be a certain way which the Doc and Janeway did. She always resisted. Chakotay let her see for herself.