Flu count is based on estimates and not positive tests. It would be much worse if they only counted confirmed cases (edit: basically double so much worse is an overstatement). They have a good understanding of the flu so the estimates are considered highly accurate. I think they consider the number of flu cases to be roughly double the number that actually go to the doctor.
Edit # 2
Here is the CDC info from last year.
an estimated 35.5 million people getting sick with influenza, 16.5 million people going to a health care provider for their illness, 490,600 hospitalizations, and 34,200 deaths from influenza (Table 1).