I don't know for a fact, but I imagine that the name comes from the idea of a "control" in a scientific experiment.
The control questions would be questions that should be easy for the subject to answer, and which are not expected to elicit any stress. The polygraph machine basically is supposed to help the interrogator monitor the subject's stress level. Different subjects will feel different amounts of stress just because of being in the room, because of whatever they may happen to be accused of, etc.
The polygraph expert forms his opinion of whether the subject answers any given question truthfully, not by looking at the subject's absolute stress level, but by comparing their stress level when answering an "important" question, vs. the subject's stress level when answering a control question. If there's no discernable difference, then the question did not cause the subject any additional stress beyond whatever baseline stress he/she was feeling just by being there and being hooked up to the machine.