You can choose to permanently trust each site's certificate as you encounter it, in which case you do not need to trust the Charles Root Certificate.
You will see a warning in your browser, or other application, when it receives that certificate because the Charles Root Certificate is not in your list of trusted root certificates. Charles generates its own certificates for sites, which it signs using a Charles Root Certificate, which is uniquely generated for your installation of Charles (as of v3.10).
