Yes, the web.xml is not supposed to change when you don't have any JAX-RS resource classes in your project. The NetBeans REST team is working on identify the cause of this problem.
This seems to be a transient behavior observed only in RC2.
I recommend upgrade to NB 6.1 FCS.
[Message sent by forum member 'ntn' (ntn)]
http://forums.java.net/jive/thread.jspa?messageID=273050