So how did Bohemian go from Czech to become counter-cultural and hippie-like? The answer is the French. In the 1400s the Roma (gypsies) reached France. The Roma came through Bohemia so the French word for Gypsy became "one who came through Bohemia" or, in French, Bohémienne.
French artists and others outside the mainstream society began moving in the poor Roma neighborhoods in the mid-1800s. It was a nineteenth century yuppie gentrification. The public then started to call these artists bohémienne. The name stuck and migrated into the English lexicon.
Demographic mass migration through the corridor of present-day Czech Republic into France is why the term Bohemian (Czech) changed it's meaning to Bohemian (counter-cultural).