Dan is the villain because the actions he is taking is causing harm to the most people.
He's ignoring Serena's declaration of love.
He's kissing Blair a married woman
Conveniently forgot about his sister Jenny exile
Puts strain on blairs and Serena's friendship
And he knows that Blair loves chuck
And he's doing a lot of underhanded stuff to make this happen
Only someone with an ulterior motive would pursue another person under these circumstances.