It doesn't take more than a few people inciting violence against a minority group to make life exceptionally difficult for them - particularly as Rastafaris are so heavily represented in the Jamaican entertainment industry.
You hit the nail on the head here. Rasta attitudes towards homosexuality are surely the result of Jamaica's view on it at large, shared by virtually all Christian sects present there, but their dominance of dancehall and other popular music genres throughout the decades puts them in a unique position of power.
I'm not one to blame media for societal ills, but the things they decide to preach from this pulpit are reprehensible in a way unmatched by American and European music. Over here there is the fortunately receding idea that gay men are inherently feminine and abnormal, which is reflected in popular music's usage of insults like f****t and queer to emasculate and display dominance over another person or concept. Over there they sing about shooting gays in the head, burning them alive and praising AIDS for killing them off. Frightening difference.