Old English scytel "a dart, arrow," from Proto-Germanic *skutilaz (source also of Old Norse skutill "harpoon"),from PIE root *skeud- "to shoot, chase, throw."
The original sense in English is obsolete; the weaving instrument so called (mid-14c.) from being "shot" across the threads. Sense of "train that runs back and forth" is first recorded 1895, from image of the weaver's instrument's back-and-forth movement over the warp; extended to aircraft 1942, to spacecraft 1969. In some other languages, the weaving instrument takes its name from its resemblance to a boat (Latin navicula, French navette, German weberschiff).
1550s, "move rapidly to and fro," from shuttle (n.); sense of "transport via a shuttle service" is recorded from 1930. Related: Shuttled; shuttling.