When deleting a startup entry, it does not matter if the item is checked or unchecked. To delete an item you highlight the item by left clicking on it and then clicking on the delete button at the top of the right pane.
However, for safety sake, I suggested that you uncheck any item that you are considering deleting to inactivate the entry and leave it that way through at least one reboot of the system. Doing that will help ensure that you are not deleting some startup entry that should not be deleted.