Stores are certainly free to arrange their toys any way they wish. Seems to me though, if I were a toy store owner, I'd arrange them in such a way that I maximize my sales. Now, I understand that in this day and age that would be perceived as waging a "War on Children", but excuse me for not giving a sh*t about that.
Was just commenting about this to my wife. We have a young baby boy and one of the marvels of his growing personality is that through no fostering of it by us, it is obvious that his has certain interests. Even before he could walk, he was obsessed with cars and trucks. It really is amazing to watch - I can't really even grasp what the appeal is to him, given that he doesn't know anything about them other than that they move. His first words were "car" and "boat". Get him in one and he'll scream unless you let him play with the steering wheel for a few minutes while he makes a "VROOM" sound.
He plays with the girls down the street and their toys might as well be invisible to him. He wanders around their playroom until he finds a ball or a car, which the girls could care less about. It's pretty funny to watch.
I'm all for letting kids pursue their interests. But don't be upset when their interests fall right in line with stereotypes that are scary to some. It's just the way it happens. There's always going to be bullies, because there's always going to be insecurity and crappy parenting. Just do your job to make your kid isn't one of them, and teach them the right way to deal with them when faced with them. They'll be fine.