Thanks for this question, Vasileia. I love to research the origin of the words we use everyday.
Java -a popular name for coffee- is named after the Java island in Indonesia. The archipelagos have the perfect weather and terroir for coffee trees and many other fruits and vegetables.
During their colonial rule, the Dutch grew coffee in Indonesia, setting the grounds for some unfair trade practices that remain even today.
Historical records place coffee plants in Indonesia in the early 1600s. Dutch colonizers didn't spend much time realizing the economic potential of coffee. As a result, they started cultivating coffee commercially, using their powerful fleet to take coffee across Europe.
Coffee quickly became an important export for Indonesia, and while Sumatra and Bali had significant coffee plantations too, Java became a synonym of coffee eventually.
How did this happen? Perhaps in the same way we call -inaccurately- certain kinds of cheeses as Parmigiano, even if they don't come from Parma. Or some wine champagne types, even if it's just a sparkling wine, far from the original French province with the same name.
So, it's very likely that Java was a popular origin among importers.
Still, Java is a great place to grow coffee and a famous region among single-origin coffee enthusiasts.
Indonesia's robusta production became prominent for some time, harming its ancient reputation for high-quality coffee. Yet, Indonesian coffee producers started growing robusta and liberica coffee trees after the worst coffee leaf rust plague ever.
In the late 1800s, coffee leaf rust destroyed many of the islands' trees, and producers replaced arabica with liberica and robusta ones in response.
Liberica and robusta coffees are more resistant to leaf rust than arabica, but they don't have many desirable characteristics. Consider that specialty robusta is a recent innovation and that most experimental processing methods and high-quality controls have been focused mainly on arabica.
Nowadays, Java has many brave and intelligent producers, as well as in many other regions in Indonesia, growing high-quality coffee that's worth trying.
In my opinion, Java is a name with such a long tradition that it deserves to be honored.