KD3PC,
The examples you listed were not science. They were a list of conclusions that people come to based on the incomplete application of the scientific method. Often, people who mistrust science do not completely understand that it is a method, not a body of knowledge.
That is, we look at empirical evidence without prejudice. You brought up bumblebees - good example. For years, scientists did not understand how bumblebees can fly. They didn't make up a reason (or claim as you did that the can't fly). They simply admitted that they didn't know yet. This is good science.
You brought up the coelacanth (assuming that's what you were referring to). It was thought to be extinct because we hadn't seen any evidence of their existence for some time. No one concluded that they existed until evidence was produced that they did. Before that, they were assumed (not known) to be extinct because there was good reason to believe that - not because it supported anyone's ideology.
As I mentioned before, it is VERY difficult to prove causation in any field. But, that doesn't warrant ignoring the evidence. Let's take gravity for example. Not only do we really not understand gravity, we are pretty sure that Newton's Law is ultimately wrong. We can't prove that a wrench dropped from 20 stories up will really fall and hit you on the head, but there is strong statistical evidence to suggest it will. So, we wear hard hats at construction sites.
People don't argue with this science because it is within the scope of their experience. With copper contamination, we're dealing with something that most people can't really relate to because they can't see it. They assume (being human) that if they can't see its effects, it must not be real.
However, there are marine biologists for whom this is not outside their scope of experience. They have the tools and knowledge to measure this. They have determined that there is a strong statistical correlation between increased copper levels and a number of adverse effects on the ecosystem. Why then, would anyone want to leech copper into the water? Could it turn out that this correlation is just a coincidence? There is a low probability of this, but it is possible. But, knowing that it is probably harmful, then why do it?
This is what I don't understand.
Let's look at lead. We don't know that lead in drinking water is harmful. We just have strong statistical correlations between elevated lead and certain health problems. Would you let your kids drink water known to be high in lead? Or, would you just conclude that it is not worth the risk?