There is and always will be fear and suspicion of "the other," the dreaded "those who aren't like us." This is why scapegoating is so effective. Who "the other" is will vary from culture to culture and time period to time period - Jews, Blacks, homosexuals, whatever. Christians are well on their way to becoming "the other" in the America of 2019.
Gays are and always have been a distinct minority. They engage in sexual activity that many non-gays find repulsive. Many of them exhibit characteristics and behaviors that are inconsistent with their gender and that make them easily identifiable. It's quite easy for any group to target them as "the other." This may be done at the societal level (e.g., the Nazis) or the individual level (e.g., redneck bullies).
On the other hand, across all time periods and virtually all cultures, homosexuality has been condemned as a perversion. This abhorrence may well be ingrained at the genetic level. Until intense political lobbying resulted in a reclassification, homosexuality was classified as a mental disorder as recently as 1973. Homosexuality was a serious criminal offense in virtually every state and country. Can this all reasonably be attributed to "homophobia," to irrational fear and loathing as though everyone in the world prior to roughly 1975 was some sort of knuckle-dragging cave man? I don't think so.
I would condemn any and all harassment or persecution of gays, which certainly has occurred just as it has occurred with other groups stigmatized as "the other." On the other hand, I am not prepared to admit that gays and gay relationships are "just like" heterosexuals and heterosexual relationships in all respects. This is what the gays demand, right now, no questions allowed.
Considering the historical classification of homosexuality as a perversion, a mental disorder and a crime, I think it is fair to say "A better and more long-term understanding of the nature of homosexuality, the nature and effects of homosexual relationships, the mental and physical health risks associated with homosexuality, the effects on children reared in homosexual households, and the effect of the acceptance of homosexuality on society as whole is needed before we decide homosexuals and homosexual relationships are 'just like' heterosexuals and their relationships."
I don't believe this can reasonably be characterized as "homophobia." A phobia is an irrational fear. I would hardly call the concerns about homosexuality - and I haven't even mentioned the religious concerns - irrational. The religious concerns likewise aren't irrational. If I strongly believed the Bible was the Word of God, and that Word condemned homosexuality as an abomination, then my vehement opposition to homosexuality would not be homophobia - it would simply be a religious conviction.