Surfer has feats to show that he too has molecular control over his body as well. One time he was in many pieces and he put himself back together (may be PIS though).
Surfer's feat of busting a planet with a mere blast>>>>>anything Thanos has ever shown in blasting power. Now don't get me wrong. Thanos power output>>>>Surfer's output on average.
Thanos has better durability too (mostly to energy blasts though and a little more than Surfer in blunt force physical attacks).
It's Surfer's versatility and speed that would make it hard for Thanos to win against him in a forum fight.
Thanos can hurt Surfer and Surfer (at his best) can hurt Thanos.
I said that about Thanos, because transmutation would have been a way to win over Thanos, but since he can control his own body, Surfer can't use this tactic.
As for the energy blast, who can say, when they are thrown, that they aren't some kind of concussion blast? Also, Thanos durability >>>>> Surfer's. A proof would be when Thor beat the shit out of him, while in Warrior Madness mode, while Thanos went toe-to-toe with him, just for shit and giggles, minutes before he incase him a pure energy block.
Speed and versatility would have been a way to win against another character, but Thanos is to far above Surfer to lose to him. And don't forget: Thanos has his own tricks in his sleave: the guy's full of gadget and device, like his shields. Shields that Surfer don't have the power to pierce. And Thanos is way, way more intelligent and cunning that Surfer, and that gives him another edge.
Thor never slammed on Thanos. Only jab like strikes connected. The slam attempt by Thor was thrawted by Thanos shield. Anyway Thanos durability is greater than Surfer's but that has nothing to do with character's not fighting at their best. Surfer jobbed to Thor.
Fights in comics hold no water if the characters were not fighting at their best as shown before. That means even though Thanos is portrayed greater than Surfer then that doesn't mean he will beat him in a forum fight when both are fighting at their best.
Surfer has many ways to beat Thanos. The reason he doesn't in comics is because the writer didn't want him to. It's easy to portray a character as superior by making another character job to them.
Surfer can pierce Thanos shields by amping, hitting them with the board at million C, black hole on them, planet busting blast on them, etc. Thanos can't attack with his shields up.