Duty-bound to make it clear that people may not play subway motorman whenever they like but wary of punishing a folk hero -- and a mere boy, at that -- law-enforcement officials settled yesterday on three years' probation for the 16-year-old who took the controls of a subway train for three and a half hours in May.

The penalty appeared not to dim the youth's dreams one whit. Leaving a Manhattan court with a plea bargain that will keep him out of jail, Keron Thomas said, "I'm going to become a train operator."

Mr. Thomas exhibited the same ingenious certainty that enabled the high school junior to take the controls of a New York City subway train and pilot it, without error, for more than three hours. Asked if he planned to obtain formal training for his passion, he said: "I don't have to study. I know what I'm doing." Dream Remains Possible

For his escapade aboard an A train, he was originally charged with four felonies, the most serious carrying a maximum penalty of seven years in prison. He pleaded guilty in Criminal Court to three misdemeanors and was sentenced to three years' probation. As a youthful offender, Mr. Thomas can claim a clean record when those three years are over and, according to the Transit Authority, will not be barred from attaining his cherished goal.