Most likely this chart represents the "relationships" as of the point of the story where Negi and his crew have confronted Godel for the first time. The proof of this:
1. The red path connecting Konoka and Setsuna.
2. No red paths connecting Negi with both Ku Fei and Chachamaru and Kotarou with Natsumi.
This character chart is only current up through chapter 250 or so. Anything after that point wouldn't be reflected in this. And I couldn't find a larger version. I've looked.