Perhaps there’s a coincidence of sounds that deceives us here: the under is not the usual word meaning "beneath," but from O.E. under, from PIE *nter- "between, among" (cf. Skt. antar "among, between," L. inter "between, among," Gk. entera "intestines;" see inter-).

http://www.etymonline.com/index.php?term=understand