In the USA, before the Civil Rights Movement really took hold in the 1960s, black people were required to sit in the 'colored section' of public buses. This was at the back of the bus, and black people were required to give up their seat to a white person if there were no available seats in the white section.
In 1955, Rosa Parks famously made stand (no pun intended) against this segregation by refusing to give up her seat to a white person. Although she wasn't the first person to do this, she was a prominent civil righs activist, and her gesture became a symbol for the civil rights movement.
Nowadays, to sit at the back of the bus has come to mean to accept unfair treatment (of oneself).