When this mode is turned on you will see a progress meter and play/pause control in the bottom left corner of your presentation. This is useful so that you can assume manual control when needed. Here's an example of how it looks in action http://slid.es/news/autoplay.
If you want a completely clean presentation without any overlaid user interface elements you can append special variables to the query string. Here's an example which will make the presentation autoplay every five seconds, as well as hide the controls and turn on looping: http://slid.es/news/background-images/fullscreen?autoSlide=5000&autoSlideStoppable=false&loop=true&controls=false&progress=false