Now I will do the “why”
Reason #1 – “On March 24, 1959, Marcello appeared before the United States Senate's McClellan Committee investigating organized crime. Serving as Chief Counsel to the committee was Robert F. Kennedy; his brother, Senator John F. Kennedy, was a member of the committee. In response to committee questioning, Marcello invoked the Fifth Amendment and refused to answer any questions relating to his background, activities, and associates. From then on, Marcello became an avowed enemy of the Kennedys.” This was the beginning of the feud between Marcello and the Kennedys. Jimmy Hoffa was in the same boat with Marcello and the Kennedy brothers. After Jimmy Hoffa got grilled in front of the committee he met up with Marcello and Trafficante afterwards and he was furious and told them something had to be done with the Kennedy brothers. Marcello and Trafficante just looked at each other knowing it was in the works.
Reason #2 - Meanwhile JFK is running for president and I mentioned previously that Joe Kennedy, his father, went to Frank Sinatra to get help from the Chicago mob, Sam Giancana, to get the Illinois vote along with West Virginia I believe. So they get the vote, JFK wins the presidency, and now the mob expects to get some special treatment but no, the Kennedy’s double cross the mob. They expected the US to take back Cuba and thus the mob gets their casinos back, but no dice, they got screwed over. Not nice to screw over the mob.
Reason #3 - You probably read that Bobby Kennedy as Attorney General basically kidnapped Marcello as he was checking into his routine immigration authorities like he did on a regular basis. Then they took him to a plane which flew him to Guatemala. He was let off the plane to fend for himself. He did have connections in Guatemala so he contacted his family and lawyer and they came down to join him. So he is down there for about two months and the US government contacts him and says they are going to let him back in to the country. So eventually he and his lawyer are traveling to El Salvador to a military prison to wait for the transportation back to the states. So then after they are traveling to an airbase where they will catch a plane back to the states. So they are traveling for sometime through jungle terrain and all of a sudden the bus pulls over and they are told to get out. The bus takes off and they are stranded in the jungle in their wingtips with not a clue where they are. They are left to fend for themselves in the jungle with no protection of any kind from wildlife. They hike along the road for miles and eventually come across a couple of kids who I believe try to mislead them but eventually they wind up at a small airport and from there they get back to the states. This happened in 1961.
So at this point Marcello hates Bobby Kennedy so much, it’s almost unbearable. So why did he go after JFK and not RFK? Because if he had gone after RFK, JFK would have used all the resources he had, which were many, to find out who killed his brother. So with JFK out of the way, LBJ is now the president and RFK is powerless as Attorney General.