I'm finishing up my freshman year and I think a lot of you guys are really overthinking this. I'm gay and I'm comfortable with my body (though it's not perfect), but I always undress for a shower in the shower stalls. Here and there I change in front of my roommates, but we never get naked.
I change in the shower stall because it's about modesty. The doors to the bathroom/showers are always wide open from the hallway, and you never know who might be walking around to catch a glimpse. It's not about sexuality or about security, it's about the fact that you're in a public place, and I don't want to see the other guys in my floor naked just like they don't want to see me naked. And I say that as a VERY openly gay man. I barely know the guys in my hall at all, but even if you knew many of them, you don't know who's comfortable with what.
In life, you have to be respectful towards EVERYONE. That means being modest. Some guys walk into the bathrooms/shower stalls wearing just boxers, which is fine by me, and I guess fine with them, but I personally prefer to be clothed. That's it. It's not about homophobia, repressed sexuality, or anything like that.