I think the location of your Startup folders may vary according to what operating system you are using. Also, I think if you have defined any users other than "System User" will have one for each user.
Simply delete any shortcuts you find in your Startup folders. Deleting a shortcut is always safe; it doesn't delete the actual program from your hard drive. You can always recreate any shortcut. Deleting the shortcut will stop the program from being started automatically when you reboot.