Actually, Captain Marvel has beaten Superman, on at least two occasions. He did it in Superman/Batman #4, and more notably, in Kingdom Come. It's worth saying that the Kingdom Come Superman was actually more powerful than the comics version typically is, and Marvel still wiped the floor with him. Superman's brute strength may be more than Marvel's, but Marvel's power is drawn from magical sources, giving him the edge.
I don't think Superman needs, by definition, to be the most powerful character around. He should be the biggest and the most visible, certainly, but not necessarily the most powerful. It's not Superman's power that gives him his status both within the main comics and the DCAU, but his ideals, his character, and the overall message of hope and strength that he conveys.
Off the top of my head, I can think of at least a few characters with strength equal to or surpassing Superman's. There's the aforementioned Captain Marvel. The Spectre could take him down, provided he had justification. A Green Lantern with the right amount of willpower might be capable of doing so. At the peak of his power (with the ability to transfer motion to other molecules), the Flash could probably swing it. Doomsday did kill him. Plastic Man could probably suffocate him. I bet Imperiex could tear him limb from limb.
Anyways, you see my point.