I agree with Brad. Discomfort isn't homophobia (or isn't always, at least) - often it's just surprise or unfamiliarity. If you were homophobic you wouldn't be here. Don't beat yourself up.
I agree that discomfort is not homophobia,
but I believe that it comes from homophobia, and it can lead to homophobia.
So when you grow up in a homophobic society, you hardly ever see gays in the streets, holding each other's hand,
or kissing. And that's because they are hiding, because society is homophobic and hates them etc etc.
So when you see that once, you are shocked, because you are not used to this.
So this is how the shock
comes from homophobia. (Not your homophobia, but society's).
Now the thing is that this shock can either stop there, or continue the cycle of the already existing homophobia.
What I am saying is, that if we are shocked, and don't want to see gays being intimate on the streets,
and we show our discomfort, then gays will continue to hide. Imagine how uncomfortable you would feel
if everybody was looking at you shocked, whenever you kissed your boyfriend.
What I am suggesting is the following: Since you have no problem with gays, and since you realize
that your reaction should not be like that at the sight of gays kissing, then you should do something to change that.
What you need IMO, is much much exposure to gays kissing/holding/whatever. You can "force" yourself
and go to gay bars, and have a drink there, and go again and again until you get used to this,
until you react to this normally, just like you react with straights.
I personally did this to myself, when I wanted to check if I would react differently at the sight of real gays in front of
me, instead of cinema/TV. It turned out that I had no discomfort at all (actually I Loved it). But in case I found out the opposite,
I was determined to go again and again, until I
cured myself.