Some (but not all) of these men identify as women and wish to live as such. Many gay men wear dresses, and enjoy doing drag. These were mostly gay men, some who wore dresses, most who did not. There were NO transgender identifying people involved in these riots.
This is huge, and she is to be celebrated as an early hero of all movements toward equal rights. She also started a movement for transvestite visibility (not transgender), which became part of the first Pride march the year following the Riots.
She played a pivotal role in the later stages of the riots, and threw things at cops during the riots. These assertions can be found in interviews with them on YouTube, and accounts from others who were there (a few are still alive). When asked about this, they clarified this repeatedly. Both of these GAY MEN identified as gay men, as men in dresses, and as transvestites. She showed up later with her friend, Sylvia Rivera. Johnson was uptown when this started, and had nothing to do with the beginning of the riots. The Riots went on for several days (June 28 – July 3, 1969). There were a few drag queens among these gay men, and none of them identified as women or transgender. The Stonewall Riots were started by the patrons of the Stonewall Inn, who were 98% gay men, and a few pissed off butch lesbians, in response to one of the police's regular raids.