If your browser supports context-menus, shipping options may be enabled or disabled right-clicking the option in the "Shipping Tables" (left) pane and selecting "Enable" or "Disable" (note: some browsers do not support this context-menu functionality):

Alternatively, you can select the shipping option you would like to enable or disable in the "Shipping Tables" (left) pane and click the "Enable Option" or "Disable Option" button above the "Shipping Tables" pane:

As you would expect, disabling a shipping option will allow you to save your settings for a shipping option while preventing it from showing up in the cart.