A lot of the reasons were cultural. The Kennedy's were an upper class Boston family while LBJ came from a poorer, rural Texas background. In 1960, before any major civil rights legislation had been passed LBJ was close with the Southern Establishment and as such distrusted by Northeast liberals.

LBJ's naked ambition turned RFK off who argued against his brother offering Johnson the VP slot in 1960. There are all sorts of rumors about how hard he fought to keep him off the ticket which came back to Johnson.

During the Kennedy administration, LBJ was sidelined in having any meaningful role in policy decisions. He was sidelined even in discussions in getting legislation passed through Congress, where his skills and expertise would have been incredibly valuable.

Johnson, with his rough, non-aristocratic style was in stark contrast to the smooth, polished Kennedys, and many in the Kennedy administration were outright cruel to him, including calling him the nickname, cornpone behind his back. As time went on, Johnson pinned much of the blame on this on RFK.

Throughout his administration, their relationship already poisoned, Johnson was deeply suspicious and paranoid about Kennedy. Since RFK had immense sympathy and popularity after his brother was killed, Johnson believed he might run against him in 64 or 68.

While Kennedy was supportive of Johnson's civil rights and anti-poverty programs, he became more and more apprehensive about Vietnam which added fuel to their rift.

When RFK was killed, Johnson to his credit did much to publicly to support the Kennedy's - helping to arrange the funeral, saying kind words publicly, and sending letters to his family, etc. Still, many Kennedy's blamed Johnson for the atmosphere in the country that led to Robert's death.