They probably using a "Mortality" number that is based on the people that are already sick.
"Mortality of those With Influenza" => Number of people that are ALREADY sick, that DIE from the disease
"Incidence" => Number of people that ACQUIRE the disease.
If you vaccinate people you reduce the number that are infected, but those that get infected anyway still have the same risk of dying. This DOES NOT mean the vaccine is ineffective, you are still reducing the number of infections in the general population and hence removing them from the risk of dying from that disease. So the "Mortality rate" is not affected but the "Incidence Rate" IS affected by around 50-60% (IIRC) which is significant.
There's also something called "herd immunity" which basically means that if a lot of people around you are immune and you are not immune your chances of acquiring the disease are lower since your peers cannot transmit it to you. So if you make enough people immune to a certain disease the rate of infection drops a lot more than you would expect, the reverse is also true... if people stop using vaccines ( say for Measels ) the risk of large outbreaks increases significantly.