With something like MRSA how do you determine that the virus is cause for disease when, as you said, many will be infected without showing symptoms?
That the root of the confusion for me. I haven't wrapped my head around how we can know a specific pathogen causes disease if a large number of people can be found to have that pathogen present without showing symptoms.
Statistics.
Not all smokers get lung cancer. But with large enough samples, smokers turn out to be much more likely to get lung cancer than non-smokers. That's why we say that smoking causes lung cancer. It's not as if someone has actually watched a particle of tobacco interact with someone's lung cells to turn them cancerous in real time.
Smoking isn't a contagious pathogen.
Second- and third-hand smoke mimic contagion.
I know as a health care worker I actually think about things like this. MRSA is a good example. Most people don't react to exposure but some do. Those that do get long term infections that are hard to get rid of if ever. Most think of this as a hospital issue. But the reality is that there are literally thousands of people with MRSA all over the world and they are carriers of it and they do things like go to the bank machine and touch it, open the door at 7-11, pick up items at the store and then put them back on the shelf and so on and so on. MRSA is literally everywhere. Some people contact it and suffer problems others do not.