Does everyone from Naruto's generation have chakra within them?
I don't blame you for asking this question. It is hard to imagine how everyone could have chakra if Kaguya was the origin of chakra, and only a few people had actually descended from Kaguya. But there are some fillers that you have not seen that will explain how.

In one of the late Shippuden episodes, we see Asura Otsusuki, the grandson of Kaguya, teach a bunch of people ninjutsu while he was on a mission to supposedly find water. I think he spread chakra by "donating" it to people. It's either that or everyone has a chakra flow that was unnoticed before Kaguya, and she activated the chakra flow and started the concept of shinobi.