Chakotay clearly had something for Janeway. She turned him down.
It seemed like a mutual decision based on their desire the get the crew home. Circumstances for all three are changed once they return. Janeway will no longer be tied to the ship and Seven will have all the options and dating opportunities the Federation can throw at her. As for Chakotay, sure no healthy male is going to turn down a young blonde when he's not in a serious relationship but after his curiousity is satisfied in that area what's to stop him from satisfying it in another.

And before anyone says he would be acting sleazy keep in mind sexual attitudes in the 25th century are a bit different...