The article says:

  > The Chicxulub crater is an impact crater buried underneath the Yucatán Peninsula in Mexico.

So I guess plate techtonics have caused things to shift around such that the crater isn't a hole in the surface now, but is underneath other rock?

Fun fact: If you google "Chicxulub crater" you see an animation of an asteroid crashing.

It was an impact crater. Over millions of years it was filled with sediment, so it's not that deep anymore.