Update README.rst

Fixed some formatting and clarified some instructions. I was editing this on the master branch before, but I figured I might want to ask permission instead of running around like I own the place.
You shouldn't have to do chmod.  I just tried it now and it works fine on Ubuntu for me.  I just downloaded it, unzipped it, went into the directory, and did ``./javaviz-server`` and it ran.  What happens when you try that?