If the one(s) you want to get rid of are ones you've downloaded/bought outside of MSTS, you can just remove the folder under C:\Program Files\Microsoft Games\Train Simulator\Routes (or wherever you installed MSTS). It might not be clear which folder corresponds to which route, though some are easier than others (for example, the NECv4's folder is named USA1a, while the default NEC is USA1). You should probably look in each folder for a readme file or something, just to make sure you're deleting the right one.
If it's one of the included routes, I don't know if you can use the uninstaller to get rid of individual routes. You might be better off doing the same thing as for an added route. A word of warning, though: if you remove one of the default routes, you might not be able to install add-on routes later, since, especially for downloaded ones, they save space by copying files from the default routes.
Overheard in NY Penn: "All aboard! Get on the train if you're coming with us!"