Once in awhile I have Naegleria scares -- a direct result of watching that episode of House a few years ago. The reality is, it's incredibly rare. Think of how many children swim and get water in their noses in freshwater ponds and lakes every summer. Infections are so rare that they make national news. The amoeba has to get WAY up into your sinus cavities for it to have any chance of reaching your brain. Unless you're using a netty pot to flush your sinuses with warm tap water, or you get water way up your nose while swimming in a fetid pond or lake during a really hot summer, you have nothing to worry about.
It's one of those extremely rare ailments that most of us would be better off just wiping from our memories.