Ian MacNaughton is listed as a director of Monty Python’s Flying Circus after directing most of the series.
MacNaughton was the programme’s principal director and producer, working on all but four of its 45 episodes. His involvement covered the series’ main BBC run from 1969 to 1974 and helped establish the visual rhythm of the show’s sketches, filmed inserts and Terry Gilliam animations.
He did not direct the first four episodes. John Howard Davies handled those programmes while MacNaughton was unavailable, after which MacNaughton became the regular director. He later directed the Pythons’ first feature film, And Now for Something Completely Different, released in 1971, and also directed the German television specials Monty Python’s Fliegender Zirkus.
John Lloyd and Michael Mills are associated with British television production, but they are not the answer to this question. Barry Took was a comedy writer and performer connected with British satire, rather than the director chiefly responsible for Flying Circus. MacNaughton’s unusually extensive episode credit is what makes him the canonical choice.