Since the opening of the BART extension to Millbrae in 2003, BART and SamTrans, instead of getting into a "marriage," it is more like getting a "divorce." Essentially BART is the parent that has the custody of the BART extension, and SamTrans is the other parent that has to pay "child support."
The marriage between BART and SamTrans actually happened years before that, when both agencies were pursuing regional and federal funds to construct the project. That was when BART and SamTrans agreed on a over-estimated ridership projection, as well as building unnecessary subways and extra station platforms which drove the cost up.
Under the agreement between both agencies, BART bills SamTrans for the operating costs based on car-miles. Therefore SamTrans has an incentive to reduce its operating subsidies by asking BART to run fewer and shorter trains. Since 2003, the service along the BART extension south of Daly City has changed a few times in order to reduce SamTrans' operating subsidies.
The current cost disputes surrounds a recent decision made by BART earlier this year to expand train length on the Dublin/Pleasanton line, which serves the SFO extension. SamTrans did not request the increase of train length, but is asked to pay for it.
Although according to the Matier and Ross article on SF Chronicle that the SFO has out-performed other stations, it is in no way meeting the original, or even revised, ridership projection made before the extension opened. In fact, the ridership was drop by 3.2% in March from last year.
Could this happen at VTA?