Unfortunately, I can't help but feel that public transport, by and large, is likely to be among the hardest of settings to make Autism/AS friendly. As I speak, the two forms of transportation that pop into my head are buses and subways.
There are a few challenges I can think of off of the top of my head.
One is that the environment within and surrounding the vehicle is always shifting. people on the spectrum do best in a controlled, predictable, unchanging environment. Unfortunately, it is the simple nature of the vehicles. They are made to allow people to enter and exit at leisure and travel through different environments. In this regard, I do not think there is much that can be done to solve the problem. The nature of public transportation means that there is probably always going to be a level of discomfort to it. Still, that doesn't mean that the discomfort can't be reduced.
Stimuli; constant, unpredictable and often overwhelming. Hear the screech of metal often present when the automatic doors open. Instantly, the off lighting and disturbing hum of florescent lighting above as strange voices and sounds reach your ears, your warning of the experience to come as you step in find one of the closely lined seats, traversing the rough reflective halls filled with shiny metal poles that reflect the colors surrounding them. There is a constant roar of the subway car passing through the tunnel or the slight tremor in the bus. Speakers burst to life on and off, making static filled announcements, as often a commercial as an important announcement about the next stop, often indistinguishable over the poor quality of the sound system. Meanwhile every time the vehicle comes to a SCREECHING stop, people decked in different colors and often affecting your senses in other ways, appear and disappear, on and off. Constant shifting movement and sounds of the city leak in. If it is night, lights will flash in and out. And if the window is tinted, one would hope it's actual tinting, rather than dots many vehicles use which can draw the eye so the watcher gets lost and overwhelmed by them. And all the while, the AC is off and it is sweltering hot or your riding in a moving Icebox.
This is what it is like for me on a public transport vehicle when everything is going right. This is what I notice.
There are some simple ways to reduce the issues related to these stimuli. One suggestion: Do something about the screeching metal noises. I think everyone would be grateful for this one but the noises sets many of us on edge like nothing else can. Tinted windows to reduce the visibility of the changes beyond the vehicle are good too. The little black dots are better than nothing, in my opinion, but not as good as true tinting. I understand the reason for the speakers but try having ones that are good enough quality that they lack static are understandable, otherwise, they are horrible random noise makers. More padding in the spaces may also help with the audio overload. I don't know what could be done about the lighting but if you can think of anything it would be a good idea to switch over. Anything to reduce the press on the senses is a good idea.