The settings are normally saved by your browser. However, they will not persist if you use private mode - your saved settings are lost when you close the window. Additionally, if you are using Safari, your settings will reset whenever you open a new chapter, since Safari does not support local storage in private mode (which is what the reader uses for storing the settings).
Something to note however is that the reader supports changing the reading direction on the fly by navigating either left or right on the first page. Both ways will go to the second page and set the reading direction accordingly.