Naegleria fowleri is close to 100% fatal,
It's close to 100% fatal once symptoms present (and are further successfully diagnosed as n. fowleri). There are confirmed instances of signs that some of the population has unknowingly gotten into their systems, so it may be significantly less than 100% fatal even when infected.
So the number to eye is about 3.5 deaths per year. So it's either the case that exposure is actually very low or else that most that get infected never even know. Pneumonia on the other hand has a much higher death count.