Yep, I attended an all boys NYC Jesuit High School from 1982-1986 and my experience is close to yours. It wouldn't be called a gay-friendly environmeent at all, but it wasn't notably hostile either.
Young people have to learn that beating on someone verbally or physically because they are different is not good.
That being said, it has come full circle: gay students in nyc now seek their own school (the Harvey Milk school) to feel safe. Esentially, self-segregation. So we as a culture went from segregation, to integration and acceptance, and then self-segregation. Silly and nutty - no student should be harmed by another student without severe consequences - that goes if the victim is too short, too fat, too skinny, too gay, too feminine, too masculine - whatever.
Ha! Some time spent in JUG would do wonders for the trouble makers!