Why rated R?

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If the infamous "f-word" is used more than once in a film, it automatically gets an R-rating. I wasn't paying too much attention to the language in this film, but I recall at least one use of that word, and I'm sure there were probably others.

Also, the content of Crumb's cartoons are very frankly sexual and, at times, many of the people in the film describe them as offensive and pornographic. These types of images are really not suitable for everyone, and so the R-rating is probably appropriate. There is also one scene in which a live (not cartoon) woman is shown with bare breasts, so that probably had something to do with it.

Because there is nudity and fat brother talks about that he use to masterbate 3 or 4 days a week

Um, did you actually look at his illustrations of sexual fantasies?

Crumb's comics have some pretty "adult" content. Not just a few breasts and buttocks but some pretty weird sexual content. This film also has references to drugs. Also parts of this film would probably disturb some people.