OK, there's a long list of reasons, each different for each brother. The major factor for JFK was anti-Catholicism. Sometimes pure ideology of neo-Nazi extremists like Hunt. Civil Rights.
JPK: Sketchy origins of wealth, pro-Nazi sentiment, anti-Semitism. The latter is consensualized, the first is disputed, and the second is basically true.
JFK
1) CR: The famous DMN 22/11/63 John Birch poster with JFK in crosshairs, accusing him of treason. Best example of that.
2) Catholicism/ Church and State: Anti-Catholic bigotry that ironically resembles anti-Semitism: "Allegiance to a foreign power/land."
3) Ideology: Many Republicans didn't like him because he was a Democrat, though Jack and Bobby were the most conservative Democrats until Clinton on many issues.
4) Assassin: deranged loony. Would've shot Nixon or Edwin Walker (his previous choices) had the opportunity occurred.
RFK
1) Civil Rights- no explanation required. Very polarizing because of 'Nam, CR and personality.
2) War: Even many Irish were incredibly abusive about Vietnam, thinking him a "vendu" to use a Quebec term that applies here.
3) Personality- Basically very *impassioned* on many issues. Listen to a speech of his or see the motorcades- security nightmares, though the assassination occurred in the opposite context, ironically.
4) Activism: You have to go to the barricades and demand change, not be complacent. Tried to convince audiences of his causes rather than convincing himself of theirs. That's why the middle class didn't feel comfortable with him (along with the motorcades) and vice versa.
4) Assassin: combination loony and Israel, of which Bobby was a strong supporter. The assassin was a Palestinian Christian, still imprisoned for life IIRC, but RFK is the most prominent victim of a Palestinian terrorist.