Everybody knows that public transit in America is a chicken and egg problem. People don't ride transit because the buses and trains aren't frequent and since people don't ride it frequently, there is no way a system can be built.
A good incentive structure should be built for commuters to ride transit. Single, one-off, my-car-is-broken rides should be discouraged by increasing single ride fares and decreasing the fares for passes.
For eg, now a daily pass costs $6 and a single ride costs $2. A person will only buy a pass if he is traveling on the system thrice. So, increase the single ride for to $2.5 and make it cumbersome to pay that fare. Decrease the day pass to $4 and make it easier for a person to buy that. Also, cut-down on the monthly fares. Once, the monthly fares go down, a lot more people ride transit and VTA can be more profitable.
Also, VTA should coordinate fare arrangements with other agencies like Amtrak, AC Transit, Caltrain etc. If someone has a VTA pass, they should be allowed to ride Amtrak/Caltrain anywhere in Santa Clara county. They should be allowed to ride the VTA for free if they have a Caltrain pass. Even though, some of these arrangements exist, not many people know about these. Some people are also frustrated because they need to pay differently at different systems. As long as a particular geography (a city or a county) is covered on one's clipper card, the person should be allowed to ride any transit regardless of whether it is bus, train or ferry.