I beleive this can all be explained. I will post my thoughts:
1) The new train line is more frequent that old bus line (1.5x), so it is not “4-5 pessengers compared to old 15”, but more like 6-8 compared to old 15 (that is pessengers transfered per same time interval). But still that is less than before.
2) You added nice bus lines to your cities. This means that people from your city centre can now get to much more places than before! And their demand for job, leisure and shopping can probably be satisfied within their own city, and much faster than going to another city. So they might switch and don’t need to go so far.
My bet is that you just need to let your cities grow a little, and gradually your train line should become much more used. You adding all those lines will definitely help cities grow, as now one can get to a lot more work, leisure and shopping places from many houses. Though you removing the road might have a negative effect on growth, for the same reason.
From my short experience, relatively small cities can be almost self-sufficient (people don’t need to go to other cities for their needs), but when you create more opportunities to go somewhere, cities start to grow and gradually people start taking those opportunities. You just have to wait.