Old English run, rune "secret, mystery, dark mysterious statement, (secret) council," also "a runic letter" (runstæf), from Proto-Germanic *runo (source also of Old Norse run "a secret, magic sign, runic character," Old High German runa "a secret conversation, whisper," Gothic runa), from PIE *ru-no-, source of technical terms of magic in Germanic and Celtic (source also of Gaelic run "a secret, mystery, craft, deceit, purpose, intention, desire," Welsh rhin "a secret, charm, virtue"). Also see Runnymede.
The presumption often is that the magical sense was the original one of the word, and the use of runes as letters was secondary. However, this derivation is questioned by some linguists: "[T]he obsession with magic of many runologists can be explained more from the psychology of the scholars than from the intrinsic contents of the inscriptions. ... [F]or almost all [of these scholars] the aura of mystery which they ascribe to the fuþark was a supplementary attraction in an otherwise austere field of labor" [French scholar Lucien Musset, quoted in Elmer H. Antonsen, "The Runes: The Earliest Germanic Writing System," in "The Origins of Writing,"University ogf Nebraska, 1989] .
The word entered Middle English as roun and by normal evolution would have become Modern English *rown, but it died out mid-15c. when the use of runes did. The modern usage is from late 17c., from German philologists who had reintroduced the word in their writings from a Scandinavian source (such as Danish rune, from Old Norse run). The runic alphabet is believed to have developed by 2c. C.E. from contact with Greek writing, with the letters modified to be more easily cut into wood or stone.