JFK was quite popular during his presidency, averaging approval ratings of 70.1% throughout, according to David Coleman's "The Fourteenth Day". From Feb. 1963, he had a 70% approval rating, reflecting the average previously stated(Pew Research Center). He was viewed favorably on his domestic and foreign policy(64% each), and 56% were satisfied with his handling of matters in Cuba. One of the the few issues where Kennedy was not that popular was in civil rights. While 55% outside the South supported the kind of equal rights legislation that Kennedy wanted, after the march on Washington, 50% said that he was pushing integration too quickly. Indeed, 63% had an unfavorable view of the March. From June onward, his popularity slipped, to 59% in October. However, most of this drop was in the South where he went from 60 to 44%, rather than up North where he saw a slighter drop, from 76 to 69%. So overall, JFK was not like Trump in terms of sentiment against him. Even areas that you wouldn't think of as being in favor of some of Kennedy's policies supported him with a decent majority until the months leading to his death.

In fact, one of the reasons that the assassination was so impactful was for the reason that Kennedy was so popular.