What does "sit in the back of the bus" mean?

The expression "sit in the back of the bus" was used here to indicate unfair treatment. In this case, unfair treatment against gay people. It probably became famous due to the Montogomery bus incident happened in 1955 where Rosa Parks, an African-American civil rights activist, was arrested for sitting in the front of the bus and not moving to the back.

A similar incident occurred couple of weeks ago where a gay couple was forced to move to the back of a bus by the driver because they were holding hands. You can read about this article here.

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).