The prefix under in understand does not mean "beneath", but rather appears to be from an unrelated root mean "among". Allow me to quote etymonline.com:
O.E. understandan "comprehend, grasp the idea of," probably lit. "stand in the midst of," from under + standan "to stand" (see stand). If this is the meaning, 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-).
That is the suggestion in Barnhart, but other sources regard the "among, between, before, in the presence of" sense of O.E. prefix and preposition under as other meanings of the same word. "Among" seems to be the sense in many O.E. compounds that resemble understand, e.g. underniman "to receive," undersecan "to investigate," underginnan "to begin." It also seems to be the sense still in expressions such as under such circumstances.
Perhaps the ultimate sense is "be close to," cf. Gk. epistamai "I know how, I know," lit. "I stand upon." Similar formations are found in O.Fris. (understonda), M.Dan. (understande), while other Germanic languages use compounds meaning "stand before" (cf. Ger. verstehen, represented in O.E. by forstanden). For this concept, most I.E. languages use figurative extensions of compounds that lit. mean "put together," or "separate," or "take, grasp" (see comprehend). O.E. oferstandan, M.E. overstonden, lit. "over-stand" seem to have been used only in literal senses.
