as far as I know it was originally a derogatory term for bikes modded to look like race bikes but were street bikes. such bikes were usually poorly built, and fairly uncomfortable makeing them less useful and really only good for looking cool parked outside or riding from one to the next of the many cafe's in most major european cities. Kinda like bar hopper choppers here in america.
eventually, it morphed to cover any generic racing style street bike. The styling of the 1979-1982 cb750F-1100F, suzuki's GS series from 1980 onward, Triumph's x75 hurricane, and kawasaki's z1r are all factory "cafe racer" style bikes drawing heavily from the home made styling of the 1970s (tracy bodies, 1/4 fairings, etc). Cafe racers differ from full on race replicas because they don't actually emulate any one particular race bike but rather draw different cues from different race bikes. The DOHC cbF's most closely emulate endurance racers of the era but were also styled to look like they had a one piece body like a drag bike, and touring handlebars and pegs (although the sport kits made them more racy).