I decided to stop my son's swimming lessons last year because he seemed to consistently get staph and candida in his upper airways. During longer breaks from swimming we could get rid of the infections, but as soon as the lessons started they reappeared. The lessons were at a pool with a good reputation. I do let him swim in a lake nearby (I once asked for a bacterial report of the lake and it seems safe) and of course in the ocean when we get a chance.
I know that in my son's school some other children are also discouraged from swimming for various reasons (skin problems for example), it's pretty common and it don't think it's overly restrictive, there are so many other things they can do.
I don't think that PA is everywhere, it's mainly in nature, especially water, and of course in hospitals. And swimming pools. For example pools in Sydney's newest swimming complex were closed for several days last year because of a PA outbreak, and there was a study of public swimming pools in Ireland, almost half of them had PA. During swimming the possibly dirty water gets in direct contact with the airways, this does not happen with boating etc.
BTW I've read that it is a common misconception that excessive mucus in CF lungs causes lung disease. The problem is that the mucus in CF lungs does not have proper bacterial killing properties (my son takes tobramycin daily to compensate for this) which leads to infection and this causes mucus build up. So if there is no infection, there is no thick mucus.