Homo- is a Greek prefix meaning same, equal, like, similar, common. Not to be confused with the Latin word homo, which which means humankind.
Phobia is an anxiety disorder characterized by extreme and irrational fear.
So, "homophobia" means an irrational fear of the same. Thus in the semantics of sexual politics, it must have been devised to describe somebody who is in frightened denial of his or her own homosexuality.
Or alternatively it is a typically illiterate import from the Americans, the Humpty Dumptys of the English language, for whom a word means what they choose it to mean.