First off, chemically speaking, it does not matter where a chemical comes from. If you distill water from sewage or sea water and get a high purity, the end product is still water. A chemical is a chemical. It has no bias and no "memory" of it's original source. This is a common misunderstanding people have regarding chemistry.
But to answer your question- no, they don't say the NaF or the NaSiF6 the government uses in the water supply comes from fertilizer plants. However, they rarely push any propaganda on us. Out of 2500 hours or so of dentistry lectures, 1-2 hours involved epidemiology pro-government crap. Last year I got into a heated debate with a guest public health official who came in to lecture the class about why water fluoridation is necessary in front of about 100 dental students and several professors. She was not prepared for this confrontation.
Believe it or not the vast majority of dental professors and classmates are very conservative. We spend a lot of time dealing with government regulations and it pisses off just about everyone. For some reason some dentists who are otherwise conservative/libertarian have a blind spot for the absurdity of water-fluoridation, but from my perspective they are coming around.
It really is not a big deal for most dentists. Water-fluoridation is pushed by a couple of hardcore public health liberal do-gooders. Most of us just ignore them.