I run several Java applications on a FreeBSD server without problems. Is there a particular subset of Java features that don't work other than on Linux? I also haven't had any issues with Java on macOS.
When I put on my pointy corporate IT hat, and I go to the Oracle web site to download Java, I see that Java runs on Linux, MacOS, Solaris, and Windows. Then when I go to download WebSphere, I see that it runs on a similar set plus AIX. Java support for Linux comes from the vendor while Java support for FreeBSD comes from the "community." Corporations will generally not depend on infrastructure that does not have reliable vendors who will sell them support contracts. Linux has this ecosystem in place. FreeBSD does not.