Edie Freedman, the designer of the O'Reilly animal covers that started the trend in the late 80s, explains why she used animals:
When I was first approached by O'Reilly to propose new covers for their books, I was immersed in the VAX/VMS world of Digital Equipment Corporation. I had heard of UNIX, but I had a very hazy idea of what it was. I had never met a UNIX programmer or tried to edit a document using vi. All of the terms associated with vi, sed and awk, uucp, lex, yacc, curses, to name just a few, sounded to me like words that might come out of a popular game called "Dungeons and Dragons." I developed a mental picture of the UNIX programmer as a "Dungeons and Dragons" player. As I started to look for imagery for the book covers, I came across some wonderful wood engravings from the 19th century. The strange animals I found seemed to be a perfect match for all those strange-sounding UNIX terms, and were esoteric enough to appeal to what I believed the UNIX programmer type to be.
When I presented the first animal covers to the people at O'Reilly, they were a bit taken aback.
"But they're so ugly!" said one.
"No one will want to pick these up!" said another.
Tim liked the quirkiness of the animals, and thought it would help to make the books stand out from other publishers' offerings. Today, the O'Reilly animal brand is well known all over the world.