I agree that phobia is a misnomer, but a lot of the English language is full of misnomers if you take root words literally. Fortunately, that's not how the language works. Homophobia, for example, refers to prejudice and dislike, not fear. Bisexual used to refer to the ability of an organism to literally become either sex, but that's not what the word means anymore.
You could use misia instead of phobia, but then most people wouldn't know what you're talking about, and we all know what one means when he or she says homophobia.
As for the original question, it depends on what one is talking about. For example, if a person has a preconceived negative opinion about homosexuality and/or homosexuals, that is prejudice, bigotry, and homophobia, all by definition. But to adequately answer the question, I would need more specifics.