Supposedly boiling isn't good enough but the reason for the concern with this type of thing is that the nasal cavities and the membranes therein are extremely sensitive and prone to infection and such infections have a direct route to the brain. Amoebas going loco in your noodle is highly unlikely but other contaminants can cause issues very counter productive to why one would use a neti pot in the first place... which is to clear the sinuses.
Also there are opinions that clearing all that goop out isn't that great to begin with. Boogers serve a purpose. Flushing things out every now and again is cool but doing it all the time might screw up a natural defense mechanism of the body.
Just gotta be careful with it. That's all. If shiz gets weird go see a doc.