In JRuby 1.6, we added support for Ruby's C API, allowing C-based extensions to build and run on JRuby.
JRuby 1.6.0 RC1 released prebuilt support for C extensions on OS X. The final release will include prebuilt support for Linux and Windows as well.
If you need C extension support on a platform for which we do not have prebuilt binaries, you'll want to grab and build JRuby yourself.
Ant should build JRuby as normal and then call "make" to build the C extension support.
Please post issues to the JRuby mailing lists, including whether extensions you use are working or not working.