LOOK. Despite all the pushing, grabing and shoving, Thor NEVER beats Loki.  [Gif from my post here]
Yes they fight each other all the time, and there are lots of punching and hitting between the two, but when you think about it, never once you see Thor beats Loki up even when he is given the chance (like the scene above). 

He never starts a fight with Loki, every single time it’s Loki who picks the fight, verbally and physcially. Thor would defend himself and fight back, but only when Loki is armed, not defenseless. Those fights that took place in Thor and the Avengers, you can see the two of them were pretty much equal, Thor was undoubtedly stronger but Loki wasn’t weak, and he had Odin’s spear in his hand, and the power from the tesseract.

But when Loki is vulnerable, Thor never takes advantage of him. 

when Thor finally got the upper hand in the fight, instead of bashing Loki with his hammer, like what he did to most people, he placed it on Loki’s chest to immobilize him. Thor was mad, because his brother was fighting him for a reason he couldn’t understand, but he didn’t want to hurt Loki, he wanted to talk to him, he wanted to understand. 

Thor tossed Loki hard onto the ground, but that was it. With all his anger and pain (having to bear the ‘death’ of his brother for I dont know how long only to find out he’s alive and trying to subjugate Earth), he could at least give Loki a punch in the face and no one could blame him. Yet he didn’t, he still wanted to talk him through, he still wanted to take him home.

Both of them were suffering from the loss of their mother, they both felt responsible of her death. And when Loki childishly blaming Thor for like everything, Thor lost his temper. Though, he couldn’t bring himself to take it on Loki, especailly when Loki was handcuffed and he was absolutlely defenseless, so he stopped.

I’ve seen many films and shows featuring two brothers, brothers always fight, and it’s very common that one ends up beating up the other.
But I doubt could Thor ever bring himself to lay a hand on Loki, and in fact, I wonder could he ever win a fight over Loki, because soon as he gains the upper hand, he stops.