In a recent episode of the Naruto anime, the reanimated Madara tries to summon the nine tails but fails since it's sealed inside Naruto, later when Madara attacks with his Deep Forest jutsu the nine tails tells Naruto,"I'd rather be controlled by you than by Madara" and shares some of its chakra with Naruto to defeat Madara. Is it really afraid of Madara or is there some other reason?
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).
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.
I think it was because that Madara was the one that made him destroy something that he didn't want to I mean come on he was basically Madara's mind controlled slave .
Watch harshirama vs Madara and you'll see why the nine tails or kurama attack the leaf village or at first tried to attack it until harshirama stop Madara by accepting his challenge to fight Madara which harshirama managed to first separate the kurama and Madara with a contact seal Justsu which freed kurama from Madara's sharingan which made kurama blind and did'nt know what was going on until he woke up and found himself locked away in the hashirama's wife mito uzumaki the first jinchuriki.
kurama was with until she became ill and so they decided to find another what they called vessel for the nine tailed fox which happened to be kushina Uzumaki the mother naruto uzumaki and the wife of minato namikaze or in other words naruto's dad and the fourth hokage which he stopped the real attack of the nine tailed fox where it was not Madara but it was another uchiha named obito that made the nine tails attack the village and then when he Lost control of kurama , kurama started attacking because of what they are treating him as but luckily naruto's dad or the fourth hokage managed to stop kurama's attack and planned to seal him in naruto on the break of death he managed to complete the seal and said his last goodbye to naruto until those times where over that's where naruto was kurama's jinchuuriki for already 16 until the attack.
So guess old memories are coming back to kurama of the times of how he was treated and he was not scared of Madara he was very angry at him and managed to help and encourage naruto by giving him some of his power to counter the deep forest Justsu and write now from naruto and kurama having a lot of issues while naruto was growing up and similar backgrounds on how they were treated they finally became friends , partners for a reason not just because they were alike to each other it's because they both wanted one and that is to protect and save the world they live in and that's why he is not afraid
9 tails fears being controlled by Madara because he likes his current host. Plain and simple. The Uchiha have a past with him as well, as depicted in shippuden episode 2 when Sasuke uses his sharingan to explore Naruto's mind.
On a side note, the Jinchuriki (all demons as well) are beings that thrive via personal gain. A demon will not present itself to a human unless it wants or needs something that can be taken or given freely from the human. Perhaps 9 tails believes Madara is just another (1)manipulative asshole with the (2)last name Uchiha. 2 reasons not to go with him. Another reason could be that e believes Madara is weak >:p and unworthy of his acquaintance.