This is entirely unsurprising. In its first year, it had a 28% drop in ridership with flat revenue but following that up in 2012 with 30% and 25% drops. Adjusted for performance of the Surfliner in general, it averaged a 30% ridership decline the first year with an 11% reduction in revenue and further drops of 25% and 27% respectively for the next year. An additional point is made that this train was one of only three trains with train-bus-train connections to the San Joaquin and the only one which allowed for an afternoon arrival in Fresno and arriving in San Francisco before 8pm. The loss of this train as a possible connection for many stations likely led to a loss of ridership and revenue on the San Joaquins as well, though it would be hard to tease out the impact of such given the phenomenal growth that the San Joaquins have experienced over the past years.
I will remain eternally puzzled as to why a slot with consistently poor on-time performance beforehand was chosen for this experiment.