rt.jar contains all of the compiled class files for the base Java Runtime environment. You should not be messing with this jar file.
For MacOS it is called classes.jar and located under /System/Library/Frameworks/<java_version>/Classes . Same not messing with it rule applies there as well :).
http://javahowto.blogspot.com/2006/05/what-does-rtjar-stand-for-in.html