Team Foundation Server's (TFS) command-line interface tf.exe workspace option maps a working folder to the server root $/ by default. That I can find, there's no way to turn this off. To combat this behavior, you'll want to unmap the default after adding in your desired folder mapping(s).
>tf workspace /new /noprompt /s:http://TFSRTM08:8080 MyWorkspace
>tf workfold $/SampleProject c:\src\SampleProject /workspace:MyWorkspace /s:http://TFSRTM08:8080
>tf workfold /unmap $/