Portability of Java helps you avoid the situation when your sysadmin tells you that he just upgraded a production server because the previous version of your distro reached its EOL and now your product does not start because libfoobar.so that you depend on is not included in the distro any more and he can't build it from source because the distro's default compiler also switched from gcc to clang.

Portability is important, even when you supposedly know your deployment platform.