Because Gamefreak wanted it that way? Well, there probably was some reasoning behind it. Maybe they felt that being Water/Flying would give it an unfair advantage against Ho-oh, which was its couterpart in GSC. In its defence, it does get quite a few Psychic attacks as well, and it isn't the only one that could potentially be three types. Has anyone else ever been caught out thinking Beedrill and Venomoth were part Flying?