Regional semantics has a lot to do with it, as well as some history.
In the US and Canada the term most often applied to the one in control is the "locomotive engineer". This has a more natural ring to, in as much as the engineer is controlling the engine and thereby the train that follows behind.
As far as history goes, many terms that are applied to North American railroads actually were hold over terms from the stage coach era of transportation, including "tie up," meaning to go off duty, "hot box," an overheated journal and "branch line," as examples.
In the UK the person behind the throttle is called the "driver," this also a term held over from the days of US equestrian propulsion. I can only assume there were drivers in the UK as well.
But, again citing north American terminology, a train is neither driven, operated nor engineered. Here the person "runs" the engine.