"The reason, I think, is basic. Doctor Who is a British program, made for a British audience, and an American Revolution story would cast Britons in the role of the story’s villains. I’m vastly oversimplifying here, I know. The point is, the Doctor’s interests in the American Revolution wouldn’t necessarily align with the Doctor Who audience’s interests."Which is true, but I'd propose, only to an extent. It is still weird. As Allyn notes at a certain point in the show's history, producers simply lost interest in making this kind of story but in the 60s, when the television iteration of Doctor Who was its most flexible and experimental, it's surprising John Lucarotti wasn't tapped to write a four parter set in Boston during the tea party, the Doctor and his companions on the opposite ends of an argument ala The Aztecs.
But even if it was perhaps too much for television, it's still amazing to me that across the Virgin New Adventures and Missing Adventures, the BBC Books Eighth Doctor novels and Past Doctor books, the various comics series and the whole of Big Finish's output, not a single writer has gone with the wind and looked at the moral ambiguities inherent in this essentially "British" in attitude alien turning up in this scenario and how his companions who almost certainly are British might react to events.
At this point, Big Finish seems the most likely venue and any combination of Doctor and Companion would react differently and be equally interesting. My taste would be for a pure historical, the moral ambiguities offering more than enough story material, but again pick a monster and wedge them in if you like. All of which said, given the co-production money, for all we know one of the bottom eight of season seven might be on this very topic. We'll see.
But if you are a writer on the franchise, I'd be interested to know why you think it's never happened.