But she also made it clear several times that she would not get involved with anyone under her command
Yes, she was true to her word, like when she said that she would return the crew on Earth.
And about Chakotay's behaviour on the unknown planet, while it left from a good intention (I think that he was really worried about his well-being, so much he built a wooden bathtub and was on the verge to build a boat), there was a strong intention to seduce Janeway and the massage was the climax.
from Chrissie's transcript site - voyager transcript (
Resolutions -
2x25)
[Shelter]
(Janeway comes out of her bedroom.)
JANEWAY: We have to talk about this.
(= the massage and the sexual atmosphere induced)
CHAKOTAY: All right.
JANEWAY: I think we need to define some parameters
(= I want to set up boundaries between you and me so that our relationship remains platonic).
CHAKOTAY: I'm not sure I can define parameters. But I can tell you a story, an ancient legend among my people. It's about an angry warrior who lived his life in conflict with the rest of his tribe, a man who couldn't find peace, even with the help of his spirit guide. For years, he struggled with his discontent. But the only satisfaction he ever got came when he was in battle. This made him a hero among his tribe, but the warrior still longed for peace within himself. One day he and his war party were captured by a neighbouring tribe led by a woman warrior. She called on him to join her because her tribe was too small and weak to defend itself from all its enemies. The woman warrior was brave and beautiful and very wise. The angry warrior swore to himself that he would stay by her side, doing whatever he could to make her burden lighter. From that point on, her needs would come first. And in that way, the warrior began to know the true meaning of peace.
(= I am there to ensure - particularly lovingly - on you and to answer ALL your desires, if you are interested),
JANEWAY: Is that really an ancient legend?
CHAKOTAY: No. But that made it easier to say.
I think that at the end of this scene, Chakotay understands that nothing will happen between them in a immediate - and beyond - future .. ., what didn't prevent him of trying again, more shyly in "Hunters"
from Chrissie's transcript site - voyager transcript (
Hunters -
4x15)
CHAKOTAY: ... . We manage to make another enemy who's going to try and hunt us down and destroy us, and on top of that
JANEWAY: It's all right. You can say it. On top of all that, I got a Dear John letter. It wasn't really a surprise. I guess I didn't really expect him to wait for me considering the circumstances. It made me realise that I was using him as a safety net, you know, as a way to avoid becoming involved with someone else.
CHAKOTAY: You don't have that safety net any more.
(= no more excuses not to pursue a romantic relationship)
JANEWAY: That's right. Then again, my life is far from uneventful here in the Delta Quadrant. It's not like I would have had a chance to pursue a relationship, even if I had realised I was alone.
CHAKOTAY: You're hardly alone, and to my way of thinking, there's still plenty of time
. (= I'm here and still madly in love with you ...and ready to wait as long as it takes)
JANEWAY: Plenty of time.
might I add an overused ice breaker with massage therapy students. It sucked the fun out of the profession. 
And then seriously, after what's happened in Scorpion, Equinox and even Endgame (pt 1), which damaged the friendship (respect and trust) that they shared - even if it was never clearly mentioned - how could these both end together?! 
