The placement of Jupiter missiles in Turkey did bother the Soviets, and was one of the reasons they sought to place them in Turkey. And the Soviets didn't like it when the US put nuclear weapons in a dozen or so other locations on its borders, either! The question of nuclear basing was a huge controversy at the time, in the sense that the Soviets protested it vigorously.
And so in a sense the US, if things were meant to be purely "just," could have said, "oh ho, you have done to us exactly what we have done to you for so long!" But of course states don't work that way; the one in the position to do something does something, and the one who doesn't, doesn't.
So in the case of Cuba it was a situation where the US 1) could limit (through a blockade) what was sent to Cuba, 2) thought it could wage war on Cuba possibly without risking general war (though this was dubious), and 3) thought that the missiles were not yet in Cuba (which turned out to be wrong, but that wasn't revealed until the 1990s). And so it used these powers to put pressure on the Soviets to withdraw the missiles. And there was, of course, a domestic political component to it: this was the Kennedy administration standing firm in front of the country and the world, trying to make a positive "moment" out of it, in a way that the earlier Berlin crisis had not quite been.
By itself, that probably wouldn't have been enough — the US quickly found that it had backed itself and the Soviets into a corner, where one wrong decision could lead to catastrophe. And the US also realized that it was going to be necessary to do some behind-the-scenes reconciliation, to give the Soviets a way out. So they offered to remove the missiles from Turkey, if the Soviets withdrew the missiles from Cuba, as a recognition, as it was, that these were roughly equivalent situations.
And if the Soviets had only been concerned about "justice," they might have refused such an offer! Because the Turkish missiles, while provocative, were nowhere nearly as deadly as the other forces that the US had on its borders. But the Turkish missiles were what was offered and what could be reasonably hoped for, and Khrushchev was looking for a way out anyway, and so that was that.