For one thing, when I picture a straight guy being uncomfortable around gay men, I wouldn't think he was homophobic. I would think he was a guy. Most striaght men don't like the idea of being gay, or have others thinking that they're gay. It's normal to feel that way, and there's nothing wrong with it. Being uncomfortable does not equal homophobic.
When you said that it made you stomach turn, that doesn't mean you're homophobic. It just means you're straight. I don't think you should be ashamed for feeling that way. If you got turned on when thinking about to people of the same sex together; it may mean you might have gay tendecies, especially if you got all hot and bothered thinking about yuri, but you don't. It's your biology talking, and just because your biology isn't the same as some one who is gay doesn't make you a bad person. Just like being gay doesn't make them a bad person.
You'd be homophobic if you hated someone just because they were gay, without even knowing them. You'd hate anything that would be associated with homosexuality. But you don't. You have friends who are gay. It's like watching your friend eat pickels with mayo and peanut butter. The thought of eating that may make your stomach churn, but does that mean you dislike your friend any less for eating it? No.
So don't worry about it. You're normal.