It's only controversial because a sizeable enough group of people have decided to vocalize it as such. It doesn't confuse a boy to paint his toenails. If anything, a child that young is probably delighted at the absurd practice of having one's toenails an oddly different color than the rest of his body. It's only when adults, with their own definitions of the symbolism behind the gesture, decide to make it a problem that it becomes anything more than a moment of humor between mother and son.
I had a discussion like this before with my grandmother and she told me of how her oldest son--who is younger than two daughters before him--used to want a baby doll because his older sisters had one. So she got him one, and he wandered around with it caring for it like a father. Eventually he grew out of it and went on to live a relatively normal life. My point with that is: Children have innocent moments of meaningless fun all the time, and a lot of the times it's the way adults react to it in their presence that suddenly shapes their definition of what they're doing beyond the "meaningless fun."