Derek, kudos to you for coming here for help, and for being supportive of your boyfriend even though this is confusing and makes you uncomfortable. Major props.
I'm not sure there's anything I can say that will smooth this over. In fact, I'm certain there's nothing I can say, because this is huge. For both of you. I have a little experience with a similar situation, since last year I came out to my straight-identified cis boyfriend, after we'd been together for five years. It was incredibly difficult, and it forced him to re-examine his entire perspective on sexuality, gender, and where he fit in with all of it. Like it seems with you and your BF, he was still very much in love with me as a person, rather than as a gender, at the time I came out. He was homophobic, uncomfortable, and confused for a while. But we talked. A lot. And we got through it. We're both happier than we've ever been, because we're both completely honest with each other about how we feel now. I'm not saying it'll work out perfectly every time. Sometimes things just don't work out. All I'm saying is that communication is the only way it will have a chance. This is true for any relationship, but for one like this especially. It's vital to let your partner know how you feel, ask him how he feels, and realize that it's OK if those feelings change over time.
Touching on pronouns (since you seem unsure which ones to use), if your SO identifies as male, using male pronouns rather than female ones may help him feel more accepted by you. Ask him what he prefers, and realize if he's very new to being "out" he may be uncomfortable asking you to use those words just yet. Touch base often, and you can keep each other much more comfortable.
One other thing I'd like to mention, too: It's tempting to start labeling right away. Labels are something you can hold onto, a fixed, familiar point when your life has been all mixed up beyond recognition. But I would encourage you to avoid identifying your self with labels anytime soon. Don't try to think of yourself as gay, or straight, or anything but Derek. You are yourself, and you love this person, who identifies as male. That's all that matters. Don't give it any of the negative connotations you may have grown up with. Just think about how you love this person, and what you'd be willing to explore with him. Give yourself permission not to worry about other people. To paraphrase Dr. Seuss, those who mind don't matter, and those who matter won't mind. The important thing, at the end of the day, is that you can respect yourself, your partner, and your decisions. The rest of the world can go be bigoted elsewhere.
I wish you both the best of luck. Feel free to PM me if you want to talk any time.