She's certainly cute, but I don't like her.

Literal

She [topic-は] certainly cute [but-が], but I [topic-は] like-is-not.

A classic concession-and-pivot structure: 確かに (concessive 'certainly') sets up the acknowledgment of an opposing point, the が ('but') pivots, and しかし ('however') intensifies the contrast. Doubling the contrast markers (が...しかし) is slightly emphatic — the speaker is making a clear separation between 'I see your point' and 'my view differs.' 好きではない is the negative of 好きだ ('like'); 好き operates as a na-adjective, so its negation is the copula's negation, not a verb's. The pattern 確かに~が、しかし~ is the standard rhetorical move for granting a premise while disagreeing with the conclusion.