Conspiracy theorists like to call just about anything a "false flag" now. But the phrase itself was not particularly common in conspiracy culture in the first decade of the 2000s. It only started to be used reflexively by theorists after a sequence of three events: the Aurora theater shooting in July 2012, the Sandy Hook School Shooting in December 2012, then the Boston Marathon Bombing of April 2013. After that there were minor spikes for a chemical weapons attack in Syria and then the shooting down of flight MH17 over the Ukraine. Then two attacks in 2015 in France (Charlie Hebdo and the Paris attacks) got the attention of Alex Jones, followed by the San Bernardino shooting and the Pulse Nightclub shooting.
These were all eclipsed by the conspiracist frenzy following the Las Vegas shooting, where it quickly became apparent it was going to be in a class of its own as a target for conspiracy theory false flag speculation. Even though a similar number of people died in the Pulse nightclub shooting, the reaction seems different.
I suspect this is due to the unfamiliarity of the perpetrator. The public had become used to mass killers being psychopathic young men or, more recently, Jihadist terrorists. A young Muslim extremist killing 49 in a gay nightclub might be a false flag, but it's not without a context that explains it. An old white man acting alone with no discernable motive just seems inexplicable, and the conspiracy mind, abhorring the inexplicable, rushes to fill the void with an explanation: a false flag, designed to take away our guns.