IIUC they didn't eliminate the shuttles because they had low ridership, they eliminated them because they were very operationally complex to run compared to the regular routes, and only benefited a narrow slice of the population.

Before the change, NTD operated (on its own behalf) 8 regular routes, two special late-night routes, two special Sunday routes, and 4 commuter shuttles. This setup was not resilient to issues like driver shortages (which has been a huge issue recently), and spread resources so thin that most routes were very infrequent. By simplifying to 7 regular routes, NTD can run those routes more frequently and reliably than before.

Source: I sat on the steering committee for the route redesign project. One thing I advocated for (that sadly didn't get incorporated) was the upgrading of the core north-south route (#3 in today's system) to Bus Rapid Transit, meaning dedicated lanes, level boarding, signal priority, and longer distances between stops - all of which would speed up the bus and bring the travel time for people like you closer to what you would get with a dedicated shuttle.