Physical Flygon is better than Special Flygon
Flygon's base attack is 100, while its base special attack is 80. That is a 20-point difference. In the tiers that Flygon is used, it's offensive sets are usually Life Orb, Choice Band, Choice Scarf, and Dragon Dance, all utilizing its physical attack.
Sure, one could use a Mixed or Full-On Special Flygon set since its special movepool has moves such as Earth Power, Draco Meteor, Giga Drain, and Fire Blast along with having a useable special attack stat, but those sets aren't generally worth using since Flygon's special moves don't have much good targets (if any) in the tiers Flygon is in. Another downside to running a Mixed or Full-Out Special Flygon set is that you can't beat some Pokemon you would otherwise beat with a Physical set. For example, Flygon's SS Analysis Page mentions that attempting a mixed of fully special Flygon moveset leaves it struggling to break past Togekiss, something a physical set can do.
Basically, while special Flygon is useable, physical Flygon is better due to the higher base attack along with Flygon's special moves not having much good targets if there are any,
Hope this helps.