In most cases, Salamence will win through pure advantage.
The first hurdle Flygon must overcome is the war of speed. Naive Salamence often run 252 Speed, meaning it's at absolute max. Flygon must be Scarfed, or a custom (and therefore non-recommended) set with a +Speed nature and 252 Speed EV's. If the latter is the case, it must then beat the Speed tie or get owned by Draco Meteor/Outrage/Dragon Claw.
The next hurdle Flygon must overcome is to not become Intimidated by Salamence. I'm not going to do calculations, but it's safe to assume a -1 Outrage won't OHKO Salamence, while Salamence will probably easily OHKO Flygon back with Draco Meteor/Outrage, and possibly with Dragon Claw as well..
So in this case, Flygon and Salamence shouldn't be sent out at the same time. That leaves Flygon few opportunities to switch in, unless you bait Salamence with a strong Steel-type that can live more than 2 unboosted Draco Meteors/Outrages/Dragon Claws.
And if you switch in, it'll likely be to a Dragon Dance. This completely screws Flygon over, as you'd have to again be running max Speed and a Choice Scarf to even hope to OHKO it, by beating the speed tie.
However, this is eased by the fact that Dragon Dance and Draco Meteor are rarely seen on the same set. However, Dragon Claw and Outrage are good substitutes that will probably do the job just as well, which can provide a lot more problems for Flygon.
Salamence will win a lot of the time, but Flygon, if given the opportunity, can triumph over Salamence.