Good news! I was able to get it to work. 
Here is what I did:
private void populateRupees(){
TiledMapTileLayer layer = (TiledMapTileLayer)map.getLayers().get(0);
tiles.clear();
for(int y = 0; y <= layer.getHeight(); y++){
for(int x = 0; x <= layer.getWidth(); x++){
Cell cell = layer.getCell(x, y);
if(cell != null){
Rectangle rect = rectPool.obtain();
rect.set(x, y, 1, 1);
tiles.add(rect);
}
}
}
Rectangle randomRect = tiles.random();
rupee.position.set(randomRect.x, randomRect.y);
}
Basically, I have an array tiles that is storing rectangles for tiles. I then go through the layer and find !null cells and add them to ‘tiles’. Once done running the loop, I create a rectangle and set it to a random entry of tiles. Once done I set the position of my coin, or rupee, to the rectangles position.
Thank you both for helping me understand this. I’m trying to learn procedural generation, which has been a very scary task, and this is helping motivate me.
=)
-A
Solved! For now…