Java coffee is made in Java, which is an island - part of INDONESIA

Java coffee is a coffee where the beans are grown and harvested in Java, the Indonesian island. However, in the U.S. many people use the term Java to describe a general coffee.

Because java is the name of the coffee bean

In order to represent the coffee in the cup it is represented with the cup

Because Java is an island where coffee is grown, as well as, American slang for coffee.

Java is one of the slang terms for coffee.