It's actually more logical that than the "everybody's gay" Yaoi logic.
You need to think in terms of an average Japanese person. That's why he thinks like that. Is kinda when you see American movies set in the fifties and the character says something racist. Maybe not blatantly racist but just a remark that passes as an everyday fact. You wouldn't think the writers, the director or the actor is racist. You would understand that it's just a portrayal of society there and then.
The same happens here. Homophobia is sometimes not even regarded as a problem in Japan and can even be grounds for dismissal. (Even tattoos can get you sacked in some companies).
So as a reaction to an openly gay person is not that bad for such a society. It is tinged with homophobia, but it's more an ignorant remark. It's based on stereotypes and what was ingrained in him by his surroundings and upbringing.
I'd like to point something out.
Page 15 > " This is Shinji-san. He's not a bad guy, but he seems to be...gay. "
Alright. This is a yaoi manga where not-so-latent homosexuality reigns supreme, and they kiss and they do naughty stuff, and they love each other like nothing's weird, BUT! They act wary around the one who's openly gay? ... (╯°Д °)╯ ╧╧ <- logic