Both are on good terms with each other, Kyoko trusts Makoto (although just for her plans against Monokuma) but Makoto puts his trust in her completely as he hopes that she would trust him as much as he trust her. Regardless, Kyoko seems to care more for Makoto as time goes on, eventually reaching to a point of having romantic feelings for him towards the end of the game.
Evidence was shown when she entered his room and told Makoto to beware of Mukuro. She also saved him from Junko (though thought to be Mukuro) who was about to kill him when he was asleep. During the last Class Trial, Makoto was the one who told the remaining students (including her) to not give in to despair, helping her overcoming her state of shock over the intense pressure of the situation they were in. Kyoko told Makoto that even though she didn't know her dad, he would never tell her to stay in the school if it meant betraying and getting him murdered by Junko, thus showing their bonds and trust to each other.
Furthermore, Kyoko also helps Makoto solve each Class Trial whenever he was out of clues. When Monokuma attempted to executed Makoto during the case of Mukuro, she risked her own life to save him out of the garbage room out of guilt for abandoning him. Also at their "Graduation," she told Makoto she was actually kind of looking forward to face whatever is out there if it's with someone like him, this hints out that she has strong romantic feelings for him.