I'm not a linguist but I think this bit of jargon leaked into tech from ham radio, which is old enough that "homebrew" (in the sense of building your own radio set from components) referred to a still-earlier time when people actually did commonly brew their own beer at home. "homespun" retains a similar meaning in general usage.
Maybe I've misunderstood pvg upthread but I assumed "'homebrew' has come to connote scrappy and hip" was about IT/tech because it doesn't have that connotation in the actual context of beer, at least to my knowledge.
