As the article points out, the infection from neti pots is apparently extremely rare.
The same infection from swimming holes is much more common, but still in the "rare" category.
As also pointed out, the goal of public water sources is to provide water safe for drinking, bathing, and other common uses. There's no practical system for assuring that all "bad stuff" is eliminated at the sources, and that nothing harmful grows in the pipes.
I'd take it just as a warning that the "more intimate" contact for the neti pot usage requires a little more care than swilling a slug of java.
But note that high water heater temperature may just boil off the chlorine (or other treatment) so that the crud grows better in the pipe to the faucet(?). Do you get a slug of cold before the hot stuff gets there? Ever turn the water off before the pipes get heated up? (Just tweakin' ya, of course.)