Your also comparing a native compiled language with an interpreted language (albeit with a very good JIT compiler). At some point of maturity, I would expect the native language to edge out Java, and when you look at the benchmarks that is generally what you see.
Except for Haskell, OCaml, Pascal and SBCL Lisp. Java is faster than all of those (on the shootout micro benchmarks), and I'd say all of them are quite mature.
From what I can tell, on the Language Shootout, only C, C++ and Fortran beat Java.
N.B. I think I only looked at benchmarks for x64 quad core.
