So just to give some context on what I'm about to write, I've worked and volunteered for a number LGBT (Lesbian/Gay/Bisexual/Transgender) organizations since I came out years ago.
First of all, "gay" is not a noun, it's an adjective describing a person. So someone can be a "gay person" but you cannot be a "gay". You'll almost never hear anyone come out by saying "I'm a gay". It's not quite like using some more derogatory terms for gay people(like a certain word that begins with F), but its definitely not PC.
Ok, now let's talk about the notion of acceptance versus tolerance. When you say that you are accepting of gays as long as it's not too in your face, then you do not accept gay people, you tolerate them. Now, don't get me wrong, this world would be a much more comfortable and safe place for members of the gay community if everyone was a bit more tolerant, but there would still be something missing because of a lack of acceptance. Imagine if you couldn't feel comfortable going out in public and being yourself, holding your partner's hand, wearing your favorite t-shirt, and so on... all because people looked at you differently whenever you did in a way that made you feel uncomfortable. That's what it's like to be tolerated, but not accepted. And that kind of discomfort can make a person very on edg and stressed out.
You have to understand, that most gay people deal with quite a bit of discrimination and homophobia in their lives, and back in the day you just couldn't be publicly gay at all without experiencing discrimination, imprisonment or worse.
What your friend did, by asking them not to make out, was remind them that they live in a world where sure, they're tolerated, but not truly accepted and all because he felt a bit of discomfort when guess what, they have to deal with that kind of discomfort on a daily basis. Now I'm not saying that it is, but consider the possibility that it might self-centered to insist that gay people cater to YOUR comfort when people rarely show them the same courtesy.
I hear lots of people say that it bothers them to see gay guys kiss, but rarely do I hear them really analyze why it bothers them. You say it bothers you on a fundamental basis... but what does that mean? Maybe the real reason is that it's just something our society trains people to be bothered by, because the general population tolerates but doesn't truly accept gay people. Think about it, if you grew up in a world where gay people making out in public was as normal as straight people doing it, do you think you'd still feel disgusted every time you saw it or would you just accept it as any other form of PDA (public displays of affection). There are lots of reasons gay affection can bother people, so ask yourself what the reason is instead of saying that it's just fundamental because that's a cop out.
Now as far as the particular incident you mentioned, yes you're friend was being intolerant. Now, if had the same reaction toward a straight couple making out in front of him, then I would say he was being intolerant of PDA, not homophobic. Now if he had been tolerant, he would've been bothered by the affection but said nothing and maybe moved to a different seat where they wouldn't have bothered him as much. If he had been accepting, he wouldn't have been bothered at all.
Now should they have responded by spitting on him? Of course not. That was an overreaction but honestly, it's hard to deal with discrimination on a regular basis without snapping every once in awhile. It's no excuse though, and they picked a fight by spitting on him. But I am curious to know exactly HOW he said it because 90% of language is body language and tone, so only 10% of what you say is the actual words that come out of your mouth. So if he had said the same words differently, it might have solicited a different reaction. Or maybe they were looking for an excuse to vent their frustration on somebody.
I guess if you take anything from this excessively long post, it should be this: If we can tolerate the fact that not everyone will accept us, you should be able to tolerate us being ourselves. It's simply unreasonable to expect us to cater to YOUR comfort level if you can't do the same for us.