I also sometimes have this “problem”… At first, it takes a while until the factory starts using the line. Click on the factory and see if there is “line used” still to “no”.
Usually, they start using the line when you have set up a route and added a vehicle…However, sometimes they still send them the direct way, or parts of it… Also, I noticed that sometimes after a while a factory stops using a route… I then realized (at least that way it looked to me) that I haven’t given enough transport capacity to a line.. (i.e. the factory has a monthly output of 30, but your track will only manage to deliver 10, then it might decide to not use the track at all)…at least, it looks to me this way. I added a few more trucks, then it was using the line again, or maybe it’s just because I updated the line and it got “initialized” again in the background.
Also, it can be sometimes a bitch, I think it’s the way the game calculate “distance”.. shortest distance usually wins..
Uncheck your vehicle from the line, then add it again… That often fixes it. The factory might decide otherwise later though …