Does anyone have a picture of where this little piece of rubber goes?

With no pic, I'm going to take a guess and assume you are talking about this piece circled in red that goes on the "B-pillar".

If it is the piece in the following pics it goes on the door.

Yes, that's the piece.  Thanks!

How much of the rubber should be visible from the outside?  Anyone have any more pics with all the trim on?

Here's your B-pillar piece:

And here's your window frame piece: