Why is the nine tails afraid of Madara?
I don't think that it's fear per-se, more like... hate.

The nine-tails prefers to help Naruto voluntarily than be forcefully controlled by Madara (or Tobi, for that matter).

Manga Spoiler:


   The bijuu have feelings, and hate being treated as weapons, ever since the Sage of Six Paths dies, Kurama has known nothing but ignorance from humans. (Like when Madara yells at him to obey, or when Hashirama tells him that he's too dangerous and he must seal him.)  


So helping Naruto was the better option.