First, if you just look at the proportions, there is no way that larger person would lose to a smaller person. Superman exceeds Kara in strength, experience, size, and training. I realize that some people think a few sparring sessions with Alex would somehow matter, but let's not forget that Superman has taken on enemies far stronger than Kara.
That's not sexism. That's simple nature.
Superman has always been portrayed as the ultimate force for good. Supergirl is a spinoff, and has never been considered his equal. The only difference is that Supergirl, in modern times, doesn't hold back, and Superman does, which could lead to a perception that Supergirl could actually win. But when Superman goes all out, Supergirl couldn't stop him.
And no, Supergirl couldn't "beat him" either. Not if Superman was going all out. The show went out of its way to make it a point that Supergirl won legitimately. In fact, Superman's sole purpose in that episode was to lose to Kara and run around telling anyone who would listen that he lost.
All that did was weaken Kara and show that she needs Superman weakened to make her look good. That's bad writing, and writers with a chip on their shoulder.