I wouldn't say he was THAT confident. JFK's popularity was waning considerably as the '64 elections approached. He was in danger of losing the South en masse (one reason that precipitated his trip to Texas to try to mend fences. He was about as popular as AIDS in Dallas, which had a very Conservative anti-JFK Republican representing it, Bruce Alger, whom is still alive today at almost 90, a year younger than JFK would be). JFK's assassination did more to bolster the Democrats than anything else. Had he lived, it was quite possible he might've lost or only narrowly prevailed, with considerably reduced Dem numbers in Congress (as it was, the Dems swept gargantuan majorities in the House and reelected most of the 1958 Senate flukes who won in reaction to Ike's 6th year).
Part of Johnson's 64 victory was, I think, sympathy votes because of the assassination, but Goldwater also came across as a crank, making jokes about lobbing missiles into the bathroom at the Kremlin, etc.
Kennedy was still convinced he would defeat Goldwater handily, but would lose to Rockefeller. Part of Goldwater's problem was that he alienated the moderates, and I think this has been a continuing problem in the Republican party. There aren't enough conservatives OR moderates to swing a national election without the other. Yet conservatives keep trying to purge moderates and moderates keep trying to purge conservatives.
I'd also point out that even the term "conservative" is up for grabs, now. Pat Buchanan and Ronald Reagan are both considered conservative, but their positions on free trade, immigration, and national defense are so far apart as to be irreconcilable.