But IIRC, they hold hands at Janeway's funeral, don't they?
Ooh, this should get a fun response...
The Chakotay/7 pairing as presented was too sudden and unexplained to make a lot of sense, but I think - in light of Seven's previously noted attraction to Chakotay - it could've been an interesting direction to explore for those characters. Walking stereotype though he be, Chakotay does have an established sensitivity/empathy and wisdom that would make him a perfectly good partner for someone who's been scarred like Seven and who's exploring her humanity. If forced to choose between Chakotay/Seven and Chakotay/Janeway... I plead the fifth, and can see reasons for both.