I understand why you'd ask yourself this question. I've always been kind of modest that way and will default to a stall if one is available when there is someone else at the urinals. So I've occasionally felt funny about it, too. In my case, I have come to feel that if they want to think I'm weirdly modest, then that's ok with me. I think in your case, if you had gone a couple stalls away, they might have just thought you were modest. I guess they could have thought you didn't want to "be next to the gay guys" but chances are they might not have, too.

Try to understand, it could have made them uncomfortable, too. It does me, sometimes if I am forced to be at a urinal next to a guy I presume to be straight. I believe I might think about this as much as you do. I'm more concerned that somehow I have a sign on my back that says "GAY!!!!" and they're going to be uncomfortable being next to me. Or worse yet, what if I accidently catch a glimpse of their dick? I am just like you in that I don't want to make the straight guys uncomfortable! (And really, I don't think it's obvious that I'm gay.) For me, it's just a lot simpler to use a stall and if they want to think anything, it's just that I'm modest.

The hint of discomfort you noticed could, you know, have been their own feeling that YOU might be uncomfortable, since you know they're gay.