My understanding is that the amoeba in question - Naegleria fowleri. - is warm water only, and seems to thrive when other circumstances kill off it competitors for food. The amoeba eats bacteria. Instances that either increase the bacterial count, or decrease the number of bacterial predators will increase the amoeba count.
For some reason, this amoeba is especially suited to entering the human body though the nasal passages.
In the WDW waterparks the water is sanitized, as required by law. Either via bromine, chlorine, or some other method (UV works, but it is big bucks). The water treatment in the water parks is not only going to kill the amoeba, but also kill its bacterial food supply. As long as you are not snorting Bay Lake, you should be good.
There was a water ski place near Orlando where you were attached to cables that would pull your across a lagoon (as opposed to a boat) that had a number of deaths. Apparently they recommended people wear nose plugs, but people were free not to. You fall when water skiing and you can get a good nose full of water.
As an aside, if you can smell chlorine in the water at a pool / park, that is a sign of not enough chlorine in the water. The chlorine will combine with organic matter to create combined chloromines, the combined cholomines are what you smell. If there is enough additional free chlorine, it will oxidize the combined chloromines, and you will have no smell. When you don't have enough free chlorine to oxidize them, then you get that "chlorine smell". And chlorine does not cause green hair either. that's from copper salts in the water.
