There are many reasons why someone might say to another "you throw like a girl," most of which cannot be attributed to personal sexism. Some bases of this "insult" are societal sexism, "roles" of the genders, and plain fact. Yet we take this observation as a big personal insult.
The main reason that people use the phrase "throwing like a girl" is that it has been incorporated into our society's vocabulary. By this phrase we mean throwing with a "head-on stance, dropped elbow, and wrist inside the elbow." If this phase was not in wide use, we might not care so much about the way we throw, but it would be a more biting and sexist insult if it were uttered.
Another reason that we can attribute to society is the general sexism of our society. Because of the way we view our children's future roles in society and the way we set up their childhood, it is easier for boys to both get a chance to throw balls and to be more accepted in so doing. Girls, on the other hand, spend more time playing with dolls and other "girlish" toys, but, curiously enough, nobody says "you play with dolls like a boy." This is due in part to our society's general attitude over the centuries that men are better than women. It is also due in greater part to the fact that it is far more likely for a girl to end up trying to throw a ball than a boy is to end up in a situation where he needs to play with dolls.
The origins of this phrase are almost definitely in the playground atmosphere of small boys. Young boys have an odd fear of girls, whether it's that they have cooties or just that they are different. The largest aspect of this fear is that almost no small boy can stand to be associated with girls, and thus the phrase "you throw like a girl" is an insult that could lead to a whole recess of teasing.
One often overlooked point on this topic is plain fact. Most girls, who never got a chance to learn how to throw "like a boy," don't throw very well. A statistical analysis would show that the average girl throws worse than the average boy, although some girls throw much better than the average boy. It has nothing to do with science, it's just a plain fact. Most people from Texas talk in a similar way, and are thus talking "like a Texan." If someone throws in a way typical of the "average" girl, that person can be said to throw like a girl.
So we see that there are many reasons why the phrase "throwing like a girl" is used. They can range from societal sexism to pure fact. It is, however, often an observation, not just an insult.