The phrase the rough, or wrong, end of the pineapple and variants mean harsh or unfair treatment.
According to the Oxford English Dictionary (3rd edition – 2006), it originated in Australia; the earliest quotation is from The Piccadilly Bushman (1961), by the Australian actor, author and producer Ray Lawler (born 1921).
While it is true that the phrase is chiefly used in Australia, I have found an instance indicating that it was in use earlier in the USA; on 3rd April 1954, the Tucson Daily Citizen (Tucson, Arizona) published the review of Clown, the autobiography of the American circus performer Emmett Kelly (1898-1979) published by Prentice Hall, New Jersey:
In Kansas City, he found himself with a small film advertising agency. It was from a drawing there that he got his idea for a hobo clown.
Later, when Kelly was actually working as a circus clown, he tried out his character, but the boss clown of the outfit didn’t like it at all. Like it or not, that is how Kelly came to create Willie, his melancholy tramp, who always gets the rough end of the pineapple but never loses hope and always keeps trying.
This extract from, and the rest of, this review contain no allusion to Australia or to Australian English. Moreover, the facts that the phrase is not in quotation marks and that the reviewer does not explain it show that that it was already well established in the USA at that time.
Ellen Connolly punned on several phrases in Fruit worker went sour, published in The Sydney Morning Herald (New South Wales, Australia) of 21st November 2001:
Matthew Smith had a plum job with greengrocer.com.au but began to think he was getting the rough end of the pineapple.
The disgruntled Web site employee deleted the firm’s systems records, causing the business to shut down for five days.
The offence carries a maximum penalty of 10 years’ jail.