Hi Melissa,
Brackets mean an optional parameter, you need not use them in the actual command line. Also, xapfile must be replaced with the actual fully-qualified .xap file name. Here is the example of the usage (note that in this example, the utility must be run from the default folder):
tcAgPatcher.exe /silent /noBackup "C:\YourSilverlightApplicationFolder\File.xap"
For more information, refer to the http://www.automatedqa.com/support/viewarticle/18829/ help topic.