This is a classic case of the difference between linguistic definition and semantic definition. To be frank, this is no different to using the prefix Mega to mean Big.
Ultimately, when we talk about grams (for instance), we're used to hearing kilograms (1k grams) and milligrams (1/1k grams) for things like bodyweight and medication concentrations respectively. These are terms that we understand and therefore don't carry any semantic connotation beyond their explicit meaning.
Micro and Mega on the other hand; these are terms that we only hear every so often. Semantically, the public see these terms as meaning REALLY small and REALLY big respectively.
Microbrewery is little more than a marketing term to mean REALLY small brewery. Smaller than even Small, which is passe, but Micro; well that must be cool.
The public on the other hand almost never hear Giga or Pico or Tera or Peta as prefixes (although that's changing with computer terminology becoming mainstream) but it's important to note that these prefixes generate an emotional connotation as much as a conceptual one in most minds that only hear the terms every so often. In that sense, their semantic usefulness becomes obvious.
To specifically answer your question, YES. It's just the heuristic application of cool terms, but the second part is not necessarily true. The person who came up with the term may well have understood what the precise meaning should have been but the reality is that they would have also known that most other people would not. The continuing use of this prefix in other applications then just adds to the semantic use of the word, and the situation becomes self-perpetuating.
In short, marketing people have a lot to answer for in terms of the misapplication of language.