H. Flu is VERY common in the under 5 set. Our CF doctor said that if you throat cultured most kids (CF or not) you'd probably find a subset that has H. Flu....a throat swab doesn't necessarily mean its in his lungs, since its such a common thing. If he starts to have symptoms it can mean that it has gotten into his lungs and should be treated.
For whatever reason, H. Flu is less of an issue as they get older and it becomes less likely to be cultured.
I know its scary to hear all these bugs and about your kiddos cultures. These bugs are EVERYWHERE!! You can't avoid them. So as CF moves forward, there will be more and more of them culturing in their lungs. Some of it is just luck, some of it is the impact of their lung mucus. I believe I read that 80% of all kids with CF will culture Pseudomonas by age 18.
Hang in there H. Flu can cause symptoms, but its usually not a big one to worry about.