Isn't the GO pass priced such that you buy it for everyone and then Caltrain hopes that peak usage isn't too high as a result? Which means you don't have enough data to evaluate if it's priced correctly or not. I bet Caltrain makes individual deals with Stanford and other large users that reflect actual usage.
Here's an interesting comparison:
48 business weeks of trips, on Clipper card: $3,456 (48•5•2•7.20)
12 monthly passes: $2,289.60 (12•190.80)
1 annual GO pass: $190 (assuming 83+ other people also use it; min. $15,960 spent per company.)
I know (from personal experience) that Stanford is a heavy GO pass user. I'm curious how many others are.
You may not need a tax. Instead, an increase in the coast of the GO pass may be enough!