The following is a summary of the major reasons why certain elements of the CIA, FBI, Military Industrial Complex including some general officers in the US military, and organized crime wanted the administration of John F. Kennedy terminated. Admittedly, they represent exclusively the perspective of those who opposed Kennedy and his policies. History has demonstrated that on virtually every issue, it was JFK who was prescient and those who opposed him that were proven wrong.
--->The CIA was angered over Kennedy's refusal to use the US military when the CIA funded Cuban exile army was defeated by Castro at the Bay of Pigs. Kennedy's firing of DCI Allen Dulles and his deputies further antagonized the CIA. It was well known by the CIA that Kennedy intended to "splinter the CIA into a thousand pieces and scatter it to the wind."
--->The National Security State was convinced that JFK was "soft on Communism" because of his attempt to end the "Cold War" including his negotiation (with Nikita Khrushchev) of the nuclear test ban treaty and his moves toward nuclear disarmament (rather than by acceding to 1) their recommended invasion of Cuba and 2) a first strike offensive nuclear attack on the USSR). The US military brass in particular objected strenously to his plans to remove all American presence from Viet Nam by 1965.
--->Kennedy was trying to eliminate the "Oil Depletion Allowance" which directly impacted the profits of Texas Oilmen who had essentially "purchased" the support of Lyndon B. Johnson a man that would gladly continue it when he became President.
--->Wall Street was concerned that JFK intended to either radically alter or end the Federal Reserve system which would severely reduce their profit stream.
--->The US military high command was higly incensed over Kennedy's handling of the Cuban Missile Crisis and his seletion of a Naval blockade rather than an all-out invasion of Cuba and or a pre-emptive nuclear attack on the Soviet Union which some of his top military commanders recommended. None favored the blockade.
--->The National Security State strongly disapproved of JFK's American University "Peace" Commencement Speech (Spring 1963) in which Kennedy made clear his decision to move toward rapproachement with the Soviet Union. Many JFK Assassination researchers believe it was this that signed his death warrant.
--->The leaders of Organized Crime felt betrayed by JFK whose brother Robert F. Kennedy the attorney general of the US was actively pursuing criminal cases against them despite the help that was provided by the Mafia (at Joseph P. Kennedy's request) in helping to elect JFK. Worse yet from their perspective is that the CIA had enlisted their help in plans to assassinate Fidel Castro of Cuba while Robert F. Kennedy was simultaneously attempting to send them to prison.
--->The major military contractors would lose many billions of dollars if JFK's plan to remove all US presence from Vietnam by 1965 was enacted. They were irate.