I think that the profitability of these investments would make a great difference in cost-effectiveness. If National Rail investments had a better rate-of-return than London city buses, then in the long run, it'll offset some of the costs of it, and vice versa. 

Is there a good way of quantifying the increased profits generated by public transportation investments?

The original website for Students for High Impact Charities (SHIC) at https://shicschools.org is down (You can find it in the Wayback Machine), but the program scripts and slides they used in high schools are still available at their google drive link at https://drive.google.com/drive/folders/0B_2KLuBlcCg4QWtrYW43UGcwajQ

Could potentially be a valuable EA community building resource