Lol. Naruto attacks she can mostly see coming and defend herself from. And then theres sasuke who can teleport her into an incoming attack. That is why she removed him. To her, he was the bigger threat at the time.
It was also Naruto's fighting style, he would distract her then attack which worked; Kakashi even said Naruto was always weirdly smart after seeing Naruto fight Kaguya 1 on 1 when he faked her out and delivered an attack. We all know Sasuke's teleporting was a big threat to her but that was all, he couldn't hurt her with PS or Amaterasu while Naruto have the speed, power, and tactics to injure Kaguya.
Also she defended herself from it everytime Sasuke used it on her with the last time being with Sakura and Kakashi helping Naruto and Sasuke.