There's been ~100 cases in 40 years. That's less than 3 people per year, so it's very rare.

There's about 10 shark attacks per year in the U.S. Now that you know that, will you stay out of the ocean forever? Or will you maybe take the risk and go for a dip if you go on a beach vacation?

edit Plus, of those 40 cases the vast majority are from swimming in lakes. So there's only a handful of cases where the infection was due to neti-pot usage. I could only find 3 confirmed cases. That's extremely rare.