I think it's important to note a quote from the article:
"Despite the inspection findings, experts stressed that there's no need for alarm, and no need to keep away from public pools."
Granted, CFers are probably at greater risk for infection than the general public, but most swimming pools probably do not pose a huge risk to us. I swam competitively (13+ hours a week in a pool) for over 10 years. Doctors believe my lung function is so high b/c of the swimming (granted, any exercise would help increase lung function, but being in the water did not hinder it).
Pretty much anything poses risks for germs...school, day care, pools, lakes, etc. You still need to live YOUR life though.
My doc recommended doing the water pik/sinus rinse each time after swimming, to make sure to get all the stuff out of my sinuses and clear them out. This has worked really well for me in significantly decreasing the number of sinus infections, so hopefully someone else finds it useful too.