The very short answer is that her experiences in Voy: Warlord (and the mental violation that went along with it) appear to have forced her to fundamentally reconsider her relationships with several of the crew, particularly her relationship with Neelix.
KES: Everything seems so different now. My thoughts and perceptions, even my relationships with my closest friends. You, the
Doctor, Neelix. How can I go back to my normal life as if nothing ever
Given that Kes has a maximum of two lines in the next 9(!) episodes it's quite hard to pinpoint exactly what happened between Kes and Neelix off-camera after the events of Warlord. The next time we gain any insight into either of their thoughts is in Voy: Darkling where we learn that Kes is planning to embark on a sexual relationship with an alien she met a few days ago.
KES: You know I've been spending time with Zahir.
JANEWAY: Yes. He seems like a very interesting young man.
KES: He is. I want to spend more time with him. A lot more time.
JANEWAY: I see.
KES: He wants to explore the Sylleran Rift. His ship travels at high warp. We could rendezvous with Voyager afterwards, before you're
too far away.
JANEWAY: That would certainly give you a chance to get to know him better.
KES: It's more than that. Captain, I've lived almost a third of my life now. I've been asking myself if I want to spend the rest of it
JANEWAY: That's certainly a legitimate question.
KES: Everyone here has been so good to me. I don't want you to think I'm ungrateful. I've just been thinking that maybe there's
more. I don't know what that means, but I know I'm changing, and I
know that there are things that I'm not satisfied with. I want
complication in my life.
The show's writers did plan to have them discuss their breakup in Voy: Fair Trade but then cut the scene (which was scripted, but evidently not filmed) for reasons of time.
There are extensive interview quotes on Memory Alpha and the scene itself is reproduced below, courtesy of the Voyager: Companion
KES: Hello, Neelix...
Neelix: Kes...I wanted to clear the air between us. It’s very apparent that our relationship has been changing ... that we aren't
close in the way we once were...
KES: I know. We seem to have ... drifted apart.
Neelix: Maybe it’s for the best. But I want you to know... you've been the finest friend anyone could have, I’ll always cherish that.
Kes: Neelix... you sound as though you're saying goodbye ... we’ll always be friends, won’t we?
Neelix: Of course. Always.
[Kes moves to him and gives him a quick kiss on the cheek — friendship
only, nothing sensual. Neelix stands like a rock and then smiles sadly
at her and EXITS. Kes looks after him, a bit puzzled.]