Spot on, and so was the article. Historically, Republicans were not the conservative party. In the late fifties, early sixties, they had two wings, the Rockefeller wing and the Goldwater wing. The Goldwater wing could almost be considered the Goldwater feather. It was never a majority of the Republican party, and Reagan is still the only member of the Goldwater wing to actually be elected, although both Bushes ran more as Reaganites than Rockefellers.
John Kennedy, before his assassination, was hoping to run against Goldwater, whom he knew he would beat easily. He felt fortunate to have run against Nixon in 1960, because Nixon was a west coast Republican. He did not believe he could beat a Republican from the Rockefeller wing of the party, either in 1960 or 1964.
The conservative Republican was an offshoot of mainstream Republicanism, with Goldwater as the prophet and Reagan as the Messiah.
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).