You weren't under a rock. Bernstein didn't come out publicly, although he lived and traveled with Cothran in a way that did cause some scandal within the profession, not to mention some distress for his daughter when Bernstein held court and partied with Cothran at Harvard for a year while she was an undergraduate (not so much because of Cothran as the way in which Bernstein was barging through his daughter's territory as she was trying to establish some independence).
Thank you for those links, Quiggin. I agree that Cothran was shortchanged in the movie, although to tell the whole story would have meant another hour, I'd say. The Napolitano article suggests that Bernstein went back to Felicia to care for her, but I have read that Bernstein and Cothran had broken up and Bernstein was back with Felicia before, but apparently very soon after, the diagnosis. (I don't remember how Maestro handles the timing.) Although i also think he was basically gay he missed his life as a pere de famille and he missed his wife. Of course today things would likely have worked out very differently.