So, this probably has a more modern explanation, but I remember learning about an Ancient Greek play, The Birds, which references a “cloud cuckoo land.” Why do we use it today? Probably one of those Victorian era cultural things that caught on.

Edit: A quick search seems to corroborate this. Also maybe the inspiration for being on “cloud nine.”

Aristophanes coined a term meaning "an unrealistic or ridiculous utopia" in his satirical play "The Birds" in 414 ce. That term was later (much later-- 1800s) translated as "Cuckoo Cloud Land" or "Cloud Cuckoo Land." It's not much of a stretch to apply the beliefs of Cloud Cuckoo Land to the cuckoos themselves. Additionally, cuckolding referred to a woman's infidelity, often as an insult to her husband (unrelated to Cloud Cuckoo Land; most likely related to the cuckoos' hiding their eggs to be raised by other birds), again, painting the poor cuckoo in a less-than-flattering light.