You're absolutely right that a lot of things contributed to their breakup. (You're also absolutely right that they're the best band in the world :) By the late 60s, they were definitely moving in different directions musically and personally.
- For the first part of their career, Brian Epstein (their manager) really held things together, and all of them more or less deferred to his decisions. Basically, they wrote the music and Brian took care of a lot of the logistics. When he died in 1967, to quote John "We've f***ing had it." Really, all 4 of the Beatles are/were great musicians, but they really didn't have any business sense. Without Brian holding them in check, there really wasn't any central leadership, and they all went off in their own directions.
- They did have a lot of personal and musical differences. As one of them (John?) explained it, they formed The Beatles when they were basically kids (just out of school), so they more or less grew up together and formed their musical ideas together. By the late 60s, they were all growing into separate individuals, and a lot of their group identity was gone.
- Yoko definitely didn't help. She was (is?) very controlling, and she tried to exert a little too much influence over the Beatles and their music. But honestly, John LET her do that- he supported her. Bottom line on Yoko, she definitely contributed to their breakup, but if it hadn't been her, it would have been someone or something else.
So yeah, there are definitely other, more complicated issues that went int their breakup. I can't tell you exactly why everyone blames Yoko, but if I had to guess, it would be either that 1) They don't really understand what all went on, and Yoko is a convenient and simple answer, or 2) It's a lot easier to just blame Yoko and not admit that the Beatles themselves caused a lot of their own problems. Either way, I'd say that Yoko Ono was just one of many factors in their breakup.