From wikipedia

Origin
In some sailing ships, speed was measured by casting the log from the stern. The log was relatively immobile, and attached by line to a reel. Some sources suggest that knots placed at a distance of 47 feet 3 inches (14.4018 m) passed through a sailor's fingers, while another used a 28 second sandglass to time the operation. The knot count would be reported and used in the sailing master's dead reckoning and navigation. This method gives a value for the knot of 20.25 in/s, or 1851.66 m/h. The difference from the accepted value today is a bit less than 0.02%.


The knots didn't fly on a rope. The rope was let out and the knots were counted.