Is foot stomping good or bad?

Ive just taken on three shetland ponies. One is a 5 year old mare with a colt at foot, and the other is a seven year old stallion. I've been surprised at how nice the stallion is, he has bonded straight away and doesn't try to assert his authority. I've noticed however, that when I go over and pet him, he sometimes puts his head down and stomps his front left hoof. Could this be some sort of passive aggression, or is it a sign that he is enjoying the cuddle?! Also, he isn't completely broken. He is halter trained, and im trying to get him to respond to pressure (poking him in the shoulder til he moves). However when i apply pressure he gets annoyed at me and sticks his head into my belly. How should I deal with this behavior? Many thanks for advice.