Protege doesn't see my plugin. The most common problem is that the plugin jar is constructed incorrectly.
Jars are essentially zip files and can be looked at with any utility that can examine zip files.
In particular, on windows you can look at the contents of a jar with WinZip. Look at the path entries for your plugin classes. The path must be exactly correct or the plugin will not be found. Go the the javasoft jar command documentation to review how to run this command. After running the jar command always look at the results with WinZip or some other utility to make sure that the jar entries have correct path.