Nonverbal communication can also be learned deliberately and if you find yourself behind at it (the worst case being autism) that's exactly what you should do. Even if you're good at it reading about how it works and consciously observing people for these nonverbal signs to learn about how it works more explicitly can give you a strong advantage in the world.
Nonverbal communication is almost more important to communication than verbal. We learn how to pick up nonverbal communication as soon as we become aware of our surroundings. Every culture and society has different nonverbal communication cues that are learned through interaction through one’s life time. Even different subgroups or friends will have different ways of nonverbal communicating.
I believe that starting from our youngest years we slowly begin to learn the art of non-verbal communication. The child's first teachers are its parents and how they react in certain situations. You can easily see children mimicking their parents facial expressions from a very young age. I think perfecting nonverbal communication takes years and years along with the ability to control your expressions.
Over time humans can quickly adapt to learning the art of nonverbal communication, being able to read some ones actions and expressions and figuring out what they are trying to communicate is a vital skill in some professions and it is something that can be learned with enough practice with it.
Nonverbal communication is an instinct that people are born with to an extent. It gets better over the years. Babies view body language and nonverbal communication in others. They don't know how to speak, and without nonverbal communication they really wouldn't be able to learn to speak or know who to be comforted by and who to be scared of.