If the above answer doesn't work, did forget to add the plugin.yml file?
If you don't add this plugin.yml file, the server will not recognise your plugin.
To do this you simply have to right click 'src' and select 'new' then 'file'. As the name, put 'plugin.yml'. Open the 'plugin.yml' file in Eclipse and use this as your 'plugin.yml' format:
main: me.<yourname>.<pluginname>.<classname>
name: <plugin name>
version: <version number>
author: <your name>
commands:
<command name>:
description: <description here>
Since you claim yourself 'new' to Java, I thought that this could be the problem.