SFO is running a special free shuttle for its 700 employees who would normally ride BART.
On July 1, the surcharge from BART to SFO went up from $1.50 to $4 one way.
"This surcharge is totally unfair to workers at this airport," said Whitfield McTair from SEIU Local 1977.
BART increased the surcharge as part of a system-wide fare increase to help close a $250 million budget deficit. The airport estimates it will cost its workers $2,000 a year.
BART says SFO should subsidize its workers' commute, just as it subsidizes higher-paid workers' parking. SFO wants BART to waive the entire surcharge; BART has offered a 25 percent discount.
"We don't want them to have to suffer economically," said BART Director Carole Ward Allen.
Ward Allen cautions those negotiations are not related to ongoing labor negotiations.
"Right now BART is dealing with so many issues and they're all getting mingled together and misinformation is going out," said Ward Allen.
Another issue on the front-burner was the Oakland airport connector. BART has approved the elevated, driver-less system, but it needs the MTC to approve the final piece of funding.
Former Senator Don Perata authored a 2004 bill to help pay for the project, but he's opposed to the current plan, saying the world and the price tag, have changed radically.
"We cannot afford a $500 million project from the Coliseum to the airport," said Perata.
BART says even with the worst-case scenario for ridership, the connector is affordable. The MTC will not vote until the end of the month at the earliest.