Ideally if the driver tells you you're distracting him, your self-preservation instinct and respect for his job dealing with traffic, etc, should be enough to make you need no further explanation, and move to the back/quiet down.
But a lot of people go through life on a hair trigger, always looking for the white whale (the intolerant bigot they can juice for years of complaining stories to their friends and to Huffington Post) - and they'll often see it when it isn't there.
So if you do like this guy did, and call two guys holding hands a distraction, or imply that it is, there's liable to be a backlash of exactly this type.
For that reason, even if I was a homophobe (and I'm not) I would just deal with it. People aren't on these shuttles for long. Just ride it out, put up with it, and keep your job.
Because again, a lot of gay people or racial minorities go through life absolutely ready to interpret anything as a slight based on their status. Everything becomes racism, everything becomes homophobia. Some will even go out of their way to try to trigger a response, be extra loud/boisterous or play into stereotypes, to try to see if they can get a rise.
Perhaps these gentlemen were laying it on thick, perhaps not. Either way, it sounds like the driver was being legitimately homophobic. And if nothing else, his own self-interest should have kicked in - and certainly his desire to not cause problems for his employer.