It was a big deal that John F. Kennedy was a Catholic when he was elected president of the USA, because of many reasons.
JFK is the first Catholic president, and there have been some fears that he would take orders from the Pope. It is very likely that a Catholic president hadn’t been chosen before him because people feared that they would take orders from the church, and they wouldn’t be able to make independent decisions. People had worried that JFK would take orders from the pope, but he has been the first person to state sincerely that being a Catholic would not interfere with being a president and that the Catholic church would have no power over him. With that, he has gained the trust of the public.
After JFK had won the West Virginia Democratic primary, with its mostly Protestant population, his religion ceased to be an issue. So, there have been a lot of prejudice towards Catholics, but that has passed on.
Here is a quote from JFK’s 1960 speech to the Greater Houston Protestant Ministerial Association
“I believe in an America where the separation of church and state is absolute, where no Catholic prelate would tell the president (should he be Catholic) how to act, and no Protestant minister would tell his parishioners for whom to vote; where no church or church school is granted any public funds or political preference; and where no man is denied public office merely because his religion differs from the president who might appoint him or the people who might elect him.”
So, there has been a lot of prejudice toward Catholics, and it has been commonly believed that Catholics adhered to the instructions of the Pope in all matter, not just religious issues. JFK broke that barrier broke that prejudice, and that is the reason that it was a big deal that he was a Catholic president.
In that time, religious authority has been more important for many people than political power and religious differences were taken more seriously than now.