The KKK, which attacked Smith and Kennedy, was against ALL Catholics. They weren't "attacking an individual like Kennedy or Obama." They were against all Catholics, and not just as President -- as residents of the United States.
There is a strong parallel in this case, even though the US isn't involved in a war with the Vatican.
(And with regard to your saying that Kennedy was a proud Catholic but Obama isn't a Muslim -- of course. But Carson wasn't speaking about Obama, as you acknowledge later. So that isn't relevant here.)
http://campaignstops.blogs.nytimes.com/2011/12/10/when-a-catholic-terrified-the-heartland/?_r=0
The response to this belief was public and private, during a campaign that lasted only two months, from September to November. Yet feelings were so strong that they swirled into a hurricane of abuse, a crescendo of fear and hate blasting through eight weeks. The school board of Daytona Beach, Fla., sent a note home with every student. It read simply: “We must prevent the election of Alfred E. Smith to the Presidency. If he is elected President, you will not be allowed to have or read a Bible.” Fliers informed voters that if Smith took the White House, all Protestant marriages would be annulled, their offspring rendered illegitimate on the spot.
Opponents blanketed the country with photos of the recently completed Holland Tunnel, the caption stating that this was the secret passage being built between Rome and Washington, to transport the pope to his new abode. Countless copies of a small cartoon appeared on lampposts and mailboxes everywhere. Titled “Cabinet Meeting — If Al Were President,” it showed the cabinet room, with the pope seated at the head of the table, surrounded by priests and bishops. Over in the corner was Al Smith, dressed in a bellboy’s uniform, carrying a serving platter, on top of which was a jug of whiskey. Summing up, the minister of the largest Baptist congregation in Oklahoma City announced, “If you vote for Al Smith you’re voting against Christ and you’ll all be damned.”
The Ku Klux Klan became actively involved in preventing a Catholic from ever getting near the White House, going all out to defeat Smith. One Klan leader mailed thousands of postcards after Democrats nominated the New Yorker, stating firmly, “We now face the darkest hour in American history. In a convention ruled by political Romanism, anti-Christ has won.” A Klan colleague in remote North Manchester, Ind., warned his audience, in booming tones, of the imminent arrival of the pope: “He may even be on the northbound train tomorrow! He may! He may! Be warned! America is for Americans! Watch the trains!” When I interviewed Hugh L. Carey, only the second Roman Catholic elected governor of New York, for my Smith biography, he remembered Klan parades in Hicksville when he was 9 years old and how frightened he was, because “there was a real anti-Catholic sentiment.”
At least as nefarious were the private conversations, whisperings that went on in homes, workplaces and schools across America. One woman wrote Franklin D. Roosevelt that she had heard that “if Governor Smith is elected president, the pope’s son will be his secretary.” F.D.R. asked, in his reply, how many sons did the lady think the pope had, and what were their occupations? Down in Amarillo, Tex., Representative Marvin Jones, a good Democrat, went into his local drugstore, and the owner asked him whom he was going to vote for. Mr. Jones answered with Smith’s name. His neighbor bluntly replied, “We’ve been fighting that bunch for 2,000 years. Do you think I’m going to turn the government over to them?”
SNIP
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