After re-watching the cutscenes of San Andreas, it seems that CJ and Ryder were on-and-off in terms of friendship. I mean while CJ was definitely closer to Big Smoke, he and Ryder seem in odds with each other. While they had their fair share of quarrels, it was really more played for humor if anything. I doubt that Ryder hated CJ or vice-versa. In fact, here are signs showing that each of them had love for each other deep down.
- During the beginning of the game, CJ walks into Ryder's place telling him that he wanted to see his homie. He even asks him for some homie love.
- In "Catalyst", Ryder compliments CJ on his efforts and vice-versa.
- During the mission "Robbing Uncle Sam", CJ and Ryder have some laughs with each other and reminisce on their past.
- At the mission "Yay-Ka-Boom-Boom", CJ is genuinely upset that he had to kill Ryder and even said out loud that was his homie.
So from what I've garnered in the story, CJ and Ryder had more of a love-hate relationship with each other and I thought that it was much more complex than any other character CJ had any relationship with. It's a shame Ryder had to turn into a traitor though, and I would've love to see how his and CJ's relationship would've evolved if not for Ryder's spontaneous betrayal.