I'm going to post this because writing is a great way of articulating thought and it might be helpful to other beginners.

If after 1.e4, black plays c5, 2.Nf3 defends the d4 square.

Now if black again attacked d4 with 2...Nc3, you could have the following exchange.

3. d4..cXd4  4. Nxd4...Nxd4,

and then 5. Qxd4

This is pracitcally the scotch game except that balck gives up his c-pawn, not his e-pawn.

Either way, the last thing black wants to do is take the white knight and lose his knight to the queen, correct?

yep.

Although on the opening explorer database I see that black has managed to win 20% of games after Qxd4.

The only reasons black would play 4...Nxd4 are surprise or he doesn't have any idea of how to play the Sicilian.