this is interesting - I did not even know there was a Websphere plugin for RHQ - where do you get it?
We have a lot of Websphere, but I don't know how RHQ would do the discovery of WAS.
WAS does not support JMX per default and it is not recommended to turn it (IMO) on unless you know what you're doing (security concerns), so WAS uses it's own management interface, much like Jboss does. I suppose the plugin would need to allow supplying credentials for WAS management.
Ok - looks like a good documentation.
Did you try restarting the RHQ Server as stated you need to do for some RHQ 4.x versions?
Also, did you add the libraries from WAS runtimes and plugins to the RHQ Agent classpath?
Do you use the default install path of WAS /opt/IBM/WebSphere/AppServer ? Not sure if it actually needs to be default but it might be necessary for discovery, not sure?