I think homophobia would be no more or less prevalent, just different.

Some straight women, particularly so-called "political lesbians", seem to view female homosexuality with a sort of benevolent-homophobia lens, similarly to how many TRAs do-- "it's so OPEN-MINDED to be a lesbian!" "Being lesbian is a choice that everybody should make!" etc. Ascribing character judgments on the basis of sexual orientation, and suggesting that sexual orientation is a choice. On the other hand, there are the heterosexual women who treat same-sex-attracted women like a disease; that's been more of my personal experience.

There is some sort of myth that women are "better" and "kinder" and "more caring" than men, so therefore they should run the world... that's some benevolent sexism bullshit. I don't think homophobia would be way less of a problem with women running the world, it would just be a different problem. The fact is, LGB people are naturally a statistical minority and so we're always going to be at a disadvantage because of that. (The same way that women are at a disadvantage compared to men because on average, they're noticeably physically weaker.)

Power-seeking groups of humans often see a smaller group as a prime target from which to steal resources and unify against; that fact alone may breed homophobia, even in the most fair, thoughtful, and ideal societies. That's just my opinion.