Am i safe from amebic meningitis if i use simply saline from the drug store?

Yes: Obviously make sure the container is sealed, no for just microbes but as a standard safety practice. Microbes as you mention can be found in warm fresh water. Most often in hot springs. However, some events have been reported from nasal flushes / rinse. However, I am not certain to the validity of these. But to make it short.. Rinse away.

Not sure how you: Are using the simply saline, but probably won't prevent amebic meningitis...