Okay, normally, most people prefer a physical Flygon, given that its Base Attack is greater than its Base Special Attack.
The reason why you may find a Special Flygon commonly, is because the difference between its Attack and Special Attack is only 20 points (at 100 and 80 respectively.
A Modest/ Timid natured Flygon is obviously a Special Sweeper, and hence.
Flygon's special move pool is way more diverse than its physical move pool, as it is seen [here].
Physical: Earthquake, Outrage, Dragon Claw, Iron Tail, Super Power and some others
Special: Earth Power, Draco Meteor, Dragon Pulse, Heat Wave, Giga Drain, Signal Beam, Fire Blast, and some others.
Obviously, you see if you're stuck with a Timid/ Modest Flygon, and with access to the Move Tutor in OR/AS, you can make the most out of such a situation.
And that, is exactly why you see Special based Flygons as well. I don't they're in the majority, but if that's what you noticed, then this might be it.