BZ trying to say that, the Juubi wasn't the one who was taking back the chakra. It was Kaguya who was taking back the chakra from her sons which were shard during their birth.
Now, what we already know is that Kaguya ate the fruit and got chakra. From her, her sons got the chakra. But then even though she was worshipped as the goddess and feared, people started stealing chakra from the God Tree. (it shows that GT didn't reacted against them)
But due to this, More Oil was spilled into the fire of ongoing war and hence Kaguya felt guilty for that. She decided to make up for her sins and became a part of the Juubi. Through Juubi she started taking back the chakra stolen by the people. After this, only people left were her sons Hamura and Hagoromo who had chakra. But she was defeated by her sons and got sealed. Then Hagoromo shared chakra among the people in the name of Ninshuu and it also got turned around........
That's why Kaguya is still gathering all the chakra.