Cartman is the target upon which Kyle vents his frustrations: with his mother, with his brother, with his teachers... but mostly with Cartman himself.
It's just... this hundred-eighty degree personality change that Cartman's gone through. It pisses him off so much—not the reformed disposition in of itself, but the way everyone acted like he'd always been that way... like Cartman'd never dressed up like Hitler, or spread his racism around town, or plotted to kill him. How could he get a free pass on that? Where was his punishment?
It's just that sometimes he gets in such a fucking rage, and the only thing that makes him feel better is smashing that asshole's face in—and why not, Cartman was the once that cultivated this deep-seated hostility; Kyle knows Cartman is the one to blame, that if he'd only treated him decently he wouldn't be the violent person he is—but then, after the initial elation, he ends up feeling so much worse.
Kyle doesn't like himself now that he doesn't have a valid reason to hate Cartman... "Eric." Oh, he has plenty of invalid reasons, and "Eric" is chief among them. It's like he's tried to divorce himself from his childhood self, deny that he was the one who did all those horrible things by renaming himself.
One day he's ripping on Cartman and Stan gives him this look and says "Christ, lay off Eric, man," and how if that fair? How is Cartman deserving of defense? Kyle just scowls and storms off to the bathroom and glares at his reflection.
He used to content himself with the knowledge that Cartman made him this way, but then, Cartman has since managed to remake himself. He used to feel justified when he beat on Cartman, like he was dealing out justice.
And now the anger wears off again, and he just feels sick. He feels like he and Cartman have had a complete role reversal, and it turns his stomach.
But if Cartman isn't The Person Who Hates Me Whom I Hate in Turn anymore, then what the hell is he? The opposite of that?...
He wonders if Cartman ever felt guilty, back when he was the bully instead of the bullied—is sure he didn't, wonders if he does now, or if, even after the conversion, he doesn't regret his past. Kyle almost hopes not. If Cartman doesn't feel guilty, then he won't have to, either. If Cartman is still horrible deep-deep-deep-deep down, then he's still in the right, and he still has a perfectly legitimate reason to hate him.