We had a big debate in Portland about whether we should add fluoride to our water (we voted it down). As far as I can tell, fluoride in the water is beneficial to people who don't brush their teeth with fluoride toothpaste, but for the majority of us who do, it's not particularly helpful.
I think people should generally have a right not to ingest substances that they don't want to, especially when said substances aren't doing anything useful and might be marginally harmful to some.
There's also an argument that all that fluoride eventually ends up accumulating in the environment, and there may be long term negative effects from that. There's no benefit from watering our lawns or flushing our toilets with fluoridated water.
So, I don't really think this is so much of a science versus anti-science debate as a question of how you should weight the costs and benefits of a policy that people can't realistically opt out of if they don't approve of it.