Tamar Haspel investigated and found that the stereotype is largely based on science:

Around the world, at all ages, boys throw better — a lot better — than girls. Studies of overhand ball throwing across different cultures have found that pre-pubescent girls throw 51 to 69 percent of the distance that boys do, at 51 to 78 percent of the velocity. As they get older, the differences increase; one U.S. study found that girls age 14 to 18 threw only 39 percent as far as boys (an average of about 75 feet vs. about 192 feet).

Researcher Jerry Thomas strongly suspects that the core difference is "something neurological". Amanda Hess isn't too concerned, since "for most modern humans … it is very rarely necessary to throw anything, ever":

But throwing remains an area of male superiority, and so it has taken on an outsized social status, from the schoolyard to the cubicle trashcan. Most prominent professional sports and recess-period feats of strength were designed by and for men, and are predicated on the idea that throwing harder, farther, and faster is better. (Mercifully, this gender divide is reversed in college, where frat boys are forced to adopt that weak-forearm motion to lob ping pong balls into red Solo cups weighted with High Life.)