I think the point NS is making is that religions are human creations.
Homophobia has to therefore be a human creation that is born out of social issues. Blaming it on religions doesn't make sense. Many religions like Hinduism don't have any scriptural issues with homosexuality. There are many non religious institutions that also are homophobic.
But they aren't new human creations generation after generation. Rather they are promulgated to the next generation through developed societal and cultural norms. You are quite right that not all societies and not all religions adopt and promulgate homophobia across generations, but many do. And in many societies over centuries religion has been a highly dominant force in creating, perpetuating and promulgating those societal norms.
And there is my further point that (many) religions claim that their homophobia isn't human derived but god derived, which is a hugely powerful tool for control of society - effectively it isn't us saying this, but god saying this and if you disobey god you will be damned forever.
It is a toxic combination that is arguably unrivalled within other societal institutions that don't claim their view is god-driven.