Why would the secret service, F.B.I ,and the C.I.A , want jhon f.k , dead?

It may have had to do with Cuba. There is a film called An American Affair which is a true story of one of JFK's girlfriends Mary Pinchot Meyer, and it shows what the issues were and how she was murdered after he was. Unfortunately, the best books on this are strangely unavailable.