If you watch the old Pride fights, you will see stomp kicks to a downed opponent quite regularly. Those are not allowed in the UFC styles rules.
The first person in the UFC (I believe) to use the foot stomp was Marco Ruas, who also was the first to use the Thai kick to great success. You will see the foot stomp with fighters that have a good ground game or takedown defense because they arent' afraid of going to the ground when they do it. Most dont' do it, but that doesn't mean it's not effective they just don't train it (anyone remember never seeing hammerfists in MMA until Sakuraba started using them?) Also, many don't use the heel portion of their foot to the small bones and those that do, you will see a good reaction of the person getting stomped moving their feet around like they are on hot rocks and focusing on getting out of that position.
It's kind of like those punches to the ribs while on the ground. To a trained guy it's not a fight ender by any means, but over time they build until you can't ignore them anymore.