Hahahahaha people are so blind, I love it.
An obvious answer to this is that Superman is more popular, yes. But that's not the only answer. The other answer is that Superman is simply more powerful. Period. He's written as more powerful, faster, with more abilities, all the time. In the time period that some of those crossovers were written, Superman was juggling planets and stopping black holes. Even in modern times, he's got the strength to affect planetary orbit.
It's like you people are asking, "Why does Jean Grey always defeat Emma Frost!? That's so odd!" Uh, Jean is more powerful than Emma. That's the way the character is written. And with the possible exception of Thor, Superman is more powerful than most of Marvel's mainstream characters. Unless the character can move planets, Superman is stronger than him. Unless the character can move at near light-speed, Superman is faster than him. I've never...ever...seen a non-cosmic Marvel character who could do either of those things.
Now I'm sure is the moment where someone will go, "Well then he's just too overpowered! It's not realistic! That's stupid!" Uh, say hello to the Sentry, who defines overpowered and unrealistic. He could beat Superman, as every Sentry fan I've ever met constantly boasts.
I don't remember anyone ever having said that Superman would beat Dr. Strange or the Silver Surfer. I don't remember it ever happening either. That would be pretty dumb.
And as anyone could tell you, the reason that Captain Marvel can beat Superman is not necessarily because of his strength and speed, which are slightly lower than Superman's, but because of his magic lightning Shazam trick. If Thor ever thought to use his god-blast, it'd be the same result.