"Aren't you assuming that 'they' didn't know about the bugs? The concept or atoms derives from ideas put forward by Greek schollars, so this is quite an assumption. "
No not an assumption but a complete lack of evidence to point to microbiology being on the agenda of the average brewer, regardless of Greek theories of atoms. Any more than the average medieval knew about man powered flight just because Leonardo managed to make some sketches about it. The miasma theory was thoroughly debunked in the 19thc yet there were still people harping on about it despite evidence.
"If you're saying that the common folk didn't know about 'bugs', how much does the modern common folk know about them? "
I would hazard that most kids in the western world are taught basic biology even at school level, they have been since at least 1930 I imagine. The overall knowledge of personal hygiene as related to health is well established at a microbial level. Again, show me the instructions about water or ale etc being carriers of disease via bacteria, rather than a general idea that 'bad' water is bad for you, so rather than an assumption it is a pretty good bet.
"I'm open to evidence either way on this ale issue, but I don't want to see one assumption debunked by using another assumption, as we might as well invent the whole thing if that's our basis. "
Er, no, as above, show me evidence that people who brewed, a huge percentage of the population, did so with an understanding of microbes that were barely theorised by a tiny amount of educated medical scholars.
If we do not have decent evidence in this we can go along the lines of show me they did not know about space travel or the combustion engine.
"I'm open to evidence either way on this ale issue"
As yet there is none supporting a knowledge of bacteria in relation to water, food, the transmission of diseases. One can only come from a 'show me they did', rather than 'show me they did not'.
Many theories existed at different times, that does not mean an automatic uptake or acceptance or wider understanding, we know that all too well. The Arabs are credited with many inventions, yet how many were taken up at a global level if at all? A singular theory does not mean practices to back it up.