This article suggests that in fact there was a habit of wearing long hair in some American gay subcultures at that time:
(Scroll down to the section “Recent meanings.”)
More precisely, there was a trend of wearing long hair among male groups perceived as being rebellious. The article talks of long hair among beatniks too. Long hair on a man meant anything long enough to touch the shoulders. Greasers were also considered rebellious in a way, even though their hair was always swept back so that it didn’t touch the collar of the shirt. My memory of the period when the Beatles first appeared was that indeed long hair just by itself was considered rebellious, even when many social groups (in small towns, say) had never personally seen anyone with hair that long.
I could easily imagine someone from those social groups saying that long hair must mean homosexuality, even if they had never met an open homosexual or seen one on TV or in the movies. Their attitude was that anyone dressing or grooming themselves differently from them must be rebellious, and all forms of rebelliousness were equal. Dressing differently, grooming oneself differently, having different political opinions, having different religious opinions, not being heterosexual, indulging in the wrong kind of stimulants, refusing to fit oneself into the segregated racial boundaries of the time, or just living in the wrong neighborhood - those were all considered rebellious, and they didn’t feel any need to distinguish them. As far as they were concerned, if you were one of those things, you might be any of them, so they didn’t feel any necessity to clarify which you were.
I remember in the early 1970’s at my rather offbeat college (New College in Sarasota, Florida) hearing people from the community summarizing the students there as being “hippie weirdo freak commie fag junkies” (or some such). The fact that one of those characteristics had nothing intrinsically to do with another of them was irrelevant to them. Their feelings were that if you accepted any one of them, you might as well being accepting them all.
Remember, too, that anyone outside the mainstream of life might wear their hair a little long, whether out of defiance or simple oversight. People making their living in the arts, live music, design, theatre, etc., would fall into that category. Some of those areas tend to have a higher incidence of gays. It’s clear from one or two of the Beatle bios that Epstein wasn’t the only gay manager. There were clearly gay men who were attracted to the music and/or the musicians; given a subculture of both gay and straight non-mainstream types it’s not surprising that someone somewhere started wearing longer than usual hair, but to say whether it came from the gay guys or the straight guys is probably futile.
Yes, but for most gay people of that period, the norm was to be very closeted . . . and to look fairly conventional, so as not to draw attention to themselves. Sure, there were small pockets of “arty” types like beatniks or musicians, but their hair was long because they were beatniksor musicians, not because they were gay. I came out in late 1963, and every single gay man I knew dressed pretty much the same as everyone else. Of course all that was to change, within a few months.