Because a lot of footy is played at a high intensity, elite footballers must be able to produce energy quickly for a sustained period of time. As such the elite footballers would genetically have a higher fast twitch to slow twitch muscle fibre ratio. This enables them to work at higher intensities for longer periods of time (produce energy anaerobically for longer). In contrast, the best long distance runners, have a higher slow twitch the fast twitch muscle fibre ratio allowing them to produce energy for longer without fatigue at lower intensities (use their aerobic energy system longer).
Combine these natural physiological factors with training effects. Long distance runners, would almost exclusively train aerobically. Which essentially result in improvements in oxygen uptake, transport and utilisation. Footballers do incorperate aerobic training in their training cycle, but they train so many other fitness components also, that their aerobic training adaptations cannot compare to the long distance runners.
You have to be very careful when using the term 'fitness' in that context. No doubt that the long distance runners have a superior aerobic capacity, however I'd be very confident that footballers are far superior to long distance runners in most, if not all, of the the remaining fitness components (muscular strength, endurance, power, anaerobic speed, etc).