Perhaps hate was a strong choice, but after reading briefly about Malcom X and his departure from the Nation of Islam, it appears as though he really did hate the guy - he's quoted as describe JFK's assassination as chickens coming home to roost.
It doesn't quite make sense to me, but I'm also very disconnected from that period of American history. Does anyone have more information about the context between these two important men?
Okay, so just a little bit of background before I get into the specifics of the JFK/Malcolm X relationship. Malcolm X wasn't aligned with the Civil Rights Movement, was extremely anti-integration, and didn't advocate a nonviolent approach to civil rights; instead, he was of the opinion that cooperation with white America would only subjugate black America further, and that violence was the only effective means of liberation.
So this is where we get to the "chickens coming home to roost" bit. That remark is part of a longer speech (available here, for your reference) titled "God's Judgment of White America". Basically, Malcolm X excoriates JFK in the speech as the head of a vast white propaganda machine that was secretly controlling the Civil Rights Movement in an attempt to use it for their own political gain and eventually destroy it from the inside out by creating divisions within it. So, when JFK was assassinated, Malcolm X saw this as an instance of white America finally being punished for its crimes. Hope this clears things up for you a bit.