Which is indeed the case in the short term. However, quitting your job means not making your rent payment for a quarter of America, so the analogy still holds.

Management bargains collectively - why can't their employees do likewise?

As in other markets, the sticky part is switching costs; one big reason employees have leverage in situations like this is that the employer can't practically fire everyone and have equally trained workers the next day. The employer then has to weigh the cost of increased wages vs. the economic harm that would be done if the business were to shut down while they found and trained new workers.

For unspecialized positions, a worker's leverage is proportional to that economic harm, not that worker's skill, or length of service, or particular suitability to the job vs. someone else. The economic harm is proportional to the economic value which was created by others, often including the public at large (e.g., power plants and transportation systems exist by laws and permits that essentially divide up natural resources owned by everyone). A moral opposition to leveraging the efforts and resources of others to enrich your own bargaining position ('hostage-taking' in anti-union parlance) is the counterargument to 'perhaps they should get paid more if the BART is so important'.

Obviously there's some middle ground here between abusive behavior on either side of a labor dispute. One idea to reach it is for both sides to have more alternatives/lower switching costs (make it more socially acceptable for workers to look for contingency jobs while already employed, and for employers to train backup workers while the positions are already nominally filled).