getClass().getResource() uses the class loader to load the resource. This means that the resource must be in the classpath to be loaded.
When doing it with Eclipse, everything you put in the source folder is "compiled" by Eclipse:
When launching the program with Eclipse, the bin directory is thus in the classpath, and since it contains the Test.properties file, this file can be loaded by the class loader, using getResource() or getResourceAsStream().
If it doesn't work from the command line, it's thus because the file is not in the classpath.
Note that you should NOT do
FileInputStream inputStream = new FileInputStream(new File(getClass().getResource(url).toURI()));
to load a resource. Because that can work only if the file is loaded from the file system. If you package your app into a jar file, or if you load the classes over a network, it won't work. To get an InputStream, just use
getClass().getResourceAsStream("Test.properties")
And finally, as the documentation indicates,
Foo.class.getResourceAsStream("Test.properties")
will load a Test.properties file located in the same package as the class Foo.
Foo.class.getResourceAsStream("/com/foo/bar/Test.properties")
will load a Test.properties file located in the package com.foo.bar.