And language changes with time and culture. A great example of this is the word ‘literally’. At this point it’s become a synonym of ‘figuratively’ with younger generations, just about the exact opposite of what it once meant. Some might argue that’s just using the word wrong, but if people are able to understand each other when using the word in that way, it’s clearly a working definition, no matter how odd.
So even if homophobia meant actually being afraid of gay people at some point, even that would be irrelevant. At the end of the day, the meaning it holds today is the only thing that’s important.