Studying the etymology of a word often reveals interesting things about the origins of the term and the thing that it refers to.
Written in the formal Japanese kanji script, the character for natto is shown above (1). Composed of two separate symbols, the first (left) translates as "to offer" and the second (right) means "bean" (2). Natto can, therefore, be translated loosely as "bean offering".
Some scholars believe that the word "natto" is derived from the older Japanese word "nassho", which means "offering place" and refers to a place in Japanese Buddhist temples where food is prepared. Historically, natto was often given as a devotional offering at Buddhist altars in temples and homes in Japan (2,3).
References: (1) Wikipedia [natto]. http://simple.wikipedia.org/wiki/Nattō. (2) History of Soybeans and Soyfoods, from 1100 BC. History of Natto and Its Relatives. Soyinfo Center. http://www.soyinfocenter.com/HSS/natto1.php. (3) Honcho Shokkan (1697) http://www.worldcat.org/title/honcho-shokkan/oclc/45145084