Boys Don't Cry, as well as the readings you mention, all have to do with interesting changes in our society in regards to GLBT issues. (GLBT, of course, means Gay, Lesbian, Bisexual, and Transgender). It is important that you be more specific about Jones' and Halberstam's pieces because both myself and other eNotes educators were unable to find them. As a result, I have to curtail my answer to an explanation of these issues within Boys Don't Cry. Put simply, this movie is a dramatization of a true story about the rape and murder about non-operative transgender man.
Brandon Teena (born Teena Brandon) is a young man, but more specifically a female-to-male, non-operative transgender man. This means that he was born a female, but has always felt completely male; therefore, he dresses and acts as a male, but has not taken the route of the transsexual operation. When his girlfriend's brother finds out that Brandon is actually a female, he is threatened by many and moves to Falls City where he befriends a lot of ex-cons. He falls in love with a girl named Lana who doesn't know that Brandon actually has female genitalia.
Brandon is eventually put into a women's prison due to previous offenses. Lana questions him about this, but Brandon stretches the truth by saying that he was born hermaphroditic (with genitalia of both sexes) and plans on a sex change to full male. At this point, a few friends learn of Brandon's birth name "Teena Brandon," and begin to suspect the truth. Lana loves Brandon regardless:
Shut up. That's your business. Look, I don't care if you're half monkey or half ape, I'm gettin' you out of here.
Now the focus switches to the actions of Tom and John, the "friends" who try to show Lena the true genitalia of Brandon. She refuses to look, but Tom and John drag Brandon off in order to both rape and beat him.
Lana: Leave him alone!
John: HIM? HIM?
Even after Brandon files a report, Tom and John still manage to find Brandon (now living in a shed) where John shoots Brandon in the head, killing him. In the fray, Tom stabs the dead Brandon before the two flee, leaving Lana to cling to Brandon's corpse.
The movie (as well as the pieces you mention) are meant to serve as a wake-up call for transgender issues for the GLBT community. Violence should never be condoned and is disgusting, no matter what a person's feelings are about people with different thoughts and feelings about gender.