Is he in for the flu or for a CF exacerbation? If the flu has settled into his lungs and he just can't kick it, then it probably exacerbated the bugs in his lungs. What does he usually culture?
HOnestly, this doesnt' necessarily mean that he'll be in again soon. CF is so unpredictable. And there is no "age they start going in" -- it really differs for every kid. My daughter has never responded well to orals, they just don't kick her staph, so when the staph acts up, we wind up trying a few orals and then going in. But lots of Cf kids are totally able to rely on orals for a very long time. There are adults on this forum that weren't hospitalized until their 20's, and others who had a lot of hospitalizations as a kid, but then it spaced out as they got older.
I'm sorry he's in patient. I hope it goes easily and he is feeling better as soon as possible.