Anonymous hacked the website in protest at the rail company's decision to disable mobile phone transmitters to hamper protests.
Bay Area Rapid Transport (Bart) took the decision on 11 August to thwart demonstrators planning to use mobile phones to co-ordinate protests against the killing of a man by transit police in July.
Anonymous retaliated by defacing Mybart.org, and posting online details of more than 2,000 of the site's users. Bart's main website, Bart.gov, was unaffected, according to the BBC.
In a message posted on the defaced website, the hacktivist group said: "We are Anonymous, we are your citizens, we are the people, we do not tolerate oppression from any government agency. Bart has proved multiple times that they have no problem exploiting and abusing the people."
The group has responded to criticism from Mybart.org users about the publication of their details online, by saying their anger should be directed at Bart for not ensuring their personal data was secure.
At the weekend, Anonymous also sympathised with rioters in England, describing the demonstrations as "a product of decades of neglect inflicted on your country by various governments," according to the Guardian.
Bart's decision to block mobile communications has met with similar criticism from civil liberties groups as UK Prime Minister David Cameron's suggestion in Parliament that access to social networks could be blocked in times of civil unrest.
His comments came after reports that some of the riots and looting had been co-ordinated using social media and encrypted text messaging services such as Blackberry Messenger.
Last week, hacker group Team Poison defaced the official website of Blackberry maker Research in Motion (RIM) after the company said it would co-operate with the UK police investigation into the riots.
The hacker group said it opposed Blackberry giving user information to police because it could lead to the wrong people being targeted.
This story was first published by Computer Weekly