The Japanese are serious about cleanliness. The word for clean is "kirei." Kirei also means pretty and/or beautiful. People often sweep the street in front of their homes. They remove their shoes in the "genkan", or entryway before entering a home. They even shower before bathing and even squat to use the bathroom to avoid touching the toilet.
If there are toilet slippers set in front of the door, it is considered bad etiquette not to use them. (Even if they’re Hello Kitty) The bathroom floor is considered dirty and so using bathroom slippers helps to confine filth. So even if you’re already wearing a pair of slippers that you put on in the entryway, take these off and put on the toilet slippers before entering.