ADDED: This is probably the best of the articles on the subject, at BBC.com, even though it contains material that doesn't make any sense to me:
In a tongue-in-cheek article, Washington Post journalist Philip Bump did some calculations around Donald Jr's statement, using data showing that the annual chance that an American would be murdered by a foreign-born terrorist was 1 in 3,609,709.A Skittle is about the volume of a quarter teaspoon. There are 3,043,261,440 quarter teaspoons in 1.5 Olympic swimming pools. So Bump seems off by a factor of 10. But even that is assuming that the terrorists are already mixed into the general populace. In Donald J. Trump Jr.'s bowl of Skittles, the bowl represents a set of would-be immigrants, 3 of whom could be terrorists. Junior's point is you'd reject the whole bowl if you knew there were 3 poison Skittles in it, no matter how much you love Skittles.
Based on his sums, it would take about one and a half Olympic swimming pools of Skittles in order to find three killers.
If the 3 Skittles were already in the the swimming pool full of Skittles, would you reject the swimming pool? That's a nonsensical question — not because the proportion is different — but because the swimming pool represents everyone in America. You can't reject the entire populace. It might make some sense — though it's not what Junior is talking about — to say you'd refuse to eat any of the purple Skittles in the swimming pool if you knew the 3 poison Skittles were purple, but you wouldn't sort through the whole swimming pool to find the all the purple Skittles and remove them. You'd just limit your eating to the non-purple Skittles.
But the fact is, we're not doing anything toward the people already in the populace that corresponds to eating the Skittles. They are just here, getting along, living their lives, until they do something that warrants attention from the authorities.
Junior's analogy has to do with rejecting adding new people to the existing populace. His point of view is: What good or ill potential is there for those of us who are already here? He's saying: We're not letting new people in for their good, but for ours. And that fits generally with the Trump position: Getting the best deal for America. What's in it for us?
Understanding the bowl-of-Skittles metaphor in that light shows the trouble: We the Americans are the people and those on the outside are just objects — lightweight throwaways to consume or toss like a piece of candy. Even if you do support Trump's idea of excluding certain sets of people, you don't have to disrespect their humanity and that's what Skittles sounds like. I know there are many people-are-food metaphors that are nice...
... but the context here is not nice, and it would be better to exhibit simple humanity.