By numerous accounts, the mafia didn't like the Kennedy ingratitude, either.
Bobby Kennedy, whom old Joe had insisted be appointed Attorney General (even though he'd never even tried a case in a courtroom) had a really wild hair up his rear about busting "organized crime" leaders. His brother got elected (with more than a little help from his father's friends) and then Bobby forgot that you're supposed to dance with the ones that brought you. Or at the very least, don't use all the power of the AG's office to go after them....
It's interesting that after his brother's assasination in Dallas, U.S. Attorney General Robert Kennedy stayed completely away from the Warren Commission investigation. He was devastated, described as being in terrible anguish for months, but the most ruthless and vindicitive of old Joe's sons wouldn't have any part in investigating his brother's murder.
Bobby supposedly knew the Mafia was involved and told a friend or two. A Notre Dame professor thought the Mafia was involved. I find the conclusions of the Warren Report and the RFK assasination too clouded.