Makoto Kousaka is an enigma. He’s a walking contradiction. He may very well be the biggest, highest-level otaku in the Genshiken, but he’s also somehow the most stylish, most sociable, and most conventionally attractive. “Normal” girls like Saki and Kanji’s sister Keiko fall for him so hard over his looks that they’re willing to tolerate his otaku tendencies.
Saki even tolerates the rest of the Genshiken just so she can be with him as much as possible.
Although every member of the Genshiken bucks stereotypes in their own way, Makoto does so in a way that bewilders everyone around him, without being off-putting.
Madarame is a high-level otaku, for sure. But he has a “refuge in audacity” way of going about things. Early on in the series, he tries to scare Saki away from the club by being over-the-top about hentai games. Makoto, though just as passionate, never makes a big deal out of it.
Makoto is comfortable, sociable, and does his thing without needing to soak it in pretense, and that goes both ways. Just like he doesn’t feel the need to change his hobbies to make Saki comfortable, he doesn’t change himself to fit the “otaku” image of his Genshiken brethren either. He acts as though the average social paradigms around otaku and “normal” people never existed. He’s comfortable going to the fashion district with Saki and going to Akihabara with the guys. He’ll cosplay a female character if he wants to. He’s even suspected of switching positions with Saki during sex so he could catch the latest episode of an anime.
In the absence of overwhelming social pressure, often the least self-conscious person is the one who sets the tone of the encounter in a social situation. And social pressure, by its nature, presses on self-consciousness. Makoto’s comfort in himself insulates him against social pressure from the people around him.
In a way, everyone else is living in Makoto’s world.
Makoto’s world is one where attractive, sociable super-otaku exist. Everyone else’s worlds don’t have room for that, so they don’t know what to do with the fact that he exists. The Genshiken are forced to accept that one of the elite among them is an ikemen. They can’t deny his power level, even despite his appearance.
In turn, “normal” people like Saki and Keiko are forced to accept that the guy they’ve fallen for is a super-otaku. They can’t deny their attraction to his looks and personality, even if his hobbies would otherwise be off-putting.
In reality, plenty of people like Makoto exist to varying degrees. Any average person you pass on the street could be an otaku and you might never know. Makoto doesn’t hide his power level, but he also doesn’t take refuge in audacity like Madarame sometimes does. If it’s brought up, he has no problem talking about the things he’s passionate about without trying to be deliberately extreme to shield himself from criticism.
Otherwise normal people accept him because he’s shown himself to be a cool person, and it turns out the otaku thing isn’t something that makes him uncool.
It should be noted that this is certainly easier done when interacting with real people in real life. When we acknowledge each other as people, we can better accept that people can’t be boiled down to 2D archetypes.
You’re not an archetype and you don’t need to fit into some arbitrary stereotype of whatever you happen to be into. If someone expects you to act a certain way because you’re into cute girl anime, that’s for them to navigate. You don’t need to live in their world. You can make them live in yours.