He doesn't necessarily counter them. Wolf actually can turn Roy into a hacky sack pretty quickly. Falcos are good at locking Roy down, too, if he slips up on spacing. Fox is fairly even, I'd say, perhaps even at a disadvantage against a well-zoned Roy.
But Roy has his advantages. His SHFFL game is 2stronk, uairs being phenomenal tools against them, and popping up space animals with dtilt is satisfying beyond belief. You can really screw up their strings with moves like jab, single hit DED, utilt and ftilt. Simply put, Roy's reach makes it very difficult for a spacey to approach safely. They can camp with blasters all they want but getting in any kill move will be a challenge.