Telepeaje Dinamico, IAVE, OHL Mexico and many others provide on line services for their prepay autopistas.
They are not only used by truckers but also by company employees and individuals. You can add money to your account on line via credit/debit and receive a factura (official invoice) via email.
The publisher I work for has all the reps company cars in the program. It avoids the employees from having to carry cash or worry about not having enough for the tolls.
The same goes with gasoline. Many Pemex franchises have the same program. This allows companies to better track their fuel consumption and keeps employees from using their cars for personal use when not authorized.
They are both good things and I've never heard a complaint. There will always be a time, like any internet or automated service to have a problem all of which can be fixed.
All the toll booths I have used for work are well-marked and the big blue signs that say "multimodal" will take cash. Some booths still take credit/cards but it depends on the concession.
Just goes to show you that in most cases if not all, the libres are just as good and as safe in some cases better than toll roads.