Pantone colors are what is called spot colors. As I understand it each spot color has its own layer in the PDF and that layer I think usually shows as black and white. The idea is that the printer will use this layer to create a printing plate for the pantone color, but it is the ink that is used on that plate that determines the color.
The printer essentially chooses color based on the name of the layer.
If you want the PDf to simulate spot colors on screen I think you need to do that manually (but I have never worked with spot colors).