I don't have any proof, but my guess as to why Kennedy was assassinated was because of his refusal to go into Cuba and Vietnam. I always saw him as the last 'real' President, the rest don't dare to seriously challenge the military-industrial complex. The message was clear enough with just a cursory investigation into his Presidency. I'd love to hear what high level, insider circles say and have said about it.
I've always convinced myself that if Bush didn't go into Iraq, he would've mysteriously met the same fate. Of course, he wasn't quite as insightful as JFK (to say the least), so there wasn't much chance he would put up a fight.