The article in FT169 states that the footprints were 3-toed, yet a Velociraptor would leave 2-toed footprints (and this is shown on Jurassic Park, when the Velociraptor nest is found, with footprints leading away from the eggshells).
Deinonychus was discovered in 1969, and its body shape, and method of killing forced palaeontologists at the time to re-evaluate their ideas, and consider dinosaurs to be warm-blooded, highly active, intelligent predators, instead of overgrown lizards.
Greg Paul, a palaeo-artist, decided Deinonychus was the same genus as Velociraptor, and so renamed it (he has since changed his mind). Since Paul's artworks were used as inspiration for the dino's in JP, this is why they used the name Velociraptor, which has since caught the public's imagination.
Incidently, the Velociraptors in the film were considerably larger than any known species at the time, but after the film was released, another type was discovered, called Utahraptor which was as large as the raptors in the film (It still doesn't have a 3 foot wide head though)