Flygon has a lot of tech options open to it, many of which can completely sway or alter match-ups, so it is useless to say any one deck "beats" it, since "it" is really split into a ton of different decks.
I think some of the most solid Flygon lists are going to run Mewtwo lv. X and Palkia lv. X. Yes, you would have to run 3 basic energy types in the deck in order to get free retreat for everything, but the control is ridiculous and since Flygon doesn't specifically need any one type to attack, it wouldn't be difficult at all to run 3 different types (1 water, 2-3 psychic, a handful of fighting). In fact, the standard 4 Roseanne's and Claydol/Cynthia's/etc. would make it rather easy.
If an SP deck doesn't want to automatically lose to Mewtwo, it has to drop Dialga G lv. X, which will then get sniped out of the equation, multiple times if necessary. Palkia helps out against everything, but especially stuff like Kingdra that runs out of steam when it can't consistently Cosmic Power.