Without more information I can only provide broad suggestions to try
to resolve the issue.
Source will be generated in the folder specified in the preference
page (default is src-gen)
The XText nature must be added to the project (you would have been
prompted to add this when opening a proto file in the project)
THe XText builder must be enabled (default is enabled)
The eclipse build process has to execute (do you have Build
Automatically on? otherwise tell the project to build)
There must be no errors in your proto file(s) - error markers will
prevent the build from running. This includes making sure and imports
are resolved (the preferences can control import directories)
Beyond those suggestions I'm not sure what might be wrong. I would
advise you to open the "Error Log" view in eclipse and see if you're
getting an error during the build process.