Here's what I commented on the article:
Going to have to completely disagree with the point on Kanji. Kanji clearly has social anxiety, and is uncomfortable around women. Being young he looks at it in a very 1 dimensional way, he thinks to himself: "I'm afraid of women, maybe I'm gay..." He thinks he's gay because he's uncomfortable around women, he comes to realization later on later on that he's just insecure and unsure. Almost everyone at some point in their life questions their sexuality regardless of their sexual orientation.
On the point of Yosuke taking a jab at Kanji on the camping trip, that seems exactly what Yosuke's character would do, because he has his own insecurities as well. That kind of prejudice exists in real life for LGBT people, and in a lot of ways it would be discourteous of the game to pretend LGBT people don't go through that sort of thing all the time, even from close friends. Yosuke saying something homophobic doesn't mean that that reflects the actual feelings of the developers, a characters are NOT just mouthpieces for the creator's in a story. Just look at Django Unchained, that movie is FULL of racist characters, does that mean Quentin Tarantino is racist? No of course not.
On the point of Naoto, I see where you're coming from, I was a little let down by the revelation that Naoto was in fact not transgender. However that does not mean the game is against transgender people, Naoto thought she had to become a man for anyone to take her seriously as a detective, she could not accept that she was in fact a women. She HATED that she was a woman, not because she felt she was supposed to be male, but because she thought she would never be taken seriously as a female detective. In the end she accepts her gender and learns something about herself. In anything Naoto's story in P4 is all about the kind of crap women have to go through in certain professions, and it's pointing out the sexism in a lot of industries/job fields.
Saying Persona 4 is "Anti-gay" is basically calling the developers homophobes based solely on your own interpretation of what was going on with the characters in the game, that's not fair at all.