Dog skittish/fearful of 20 month old son

We have a 3 year old mixed dog and she is really good with our 20 month old son, they play tug together and he throws balls to her. However when our son wants to cuddle or even stroke her she runs a mile and gets really skittish if 'cornered'. We never leave them together alone and I know she would never lash out, but our son absolutely loves her and all dogs and I was wondering if theres a way to get her used to him a bit more. She loves strokes and cuddles from me and OH so I know its not a 'space' thing. Just don;t know what to do.
Our son went through a 'throwing' stage and has hit all of us including the dog with cars/balls etc. But we made sure that we told him off infront of the dog so that she knew that she did nothing wrong and we gave her lots of cuddles and made our son appologise to her by giving her a little stroke (while we cuddled her). I don't think it was this that effected her as she was like this before the throwing stage.
Any help or pointers would be appreciated!

At the risk of stating the obvious & as you're aware, you should never leave a dog & child unattended, no matter how good the dog, or how well-behaved the child.

But despite doing everything you can to ensure that your son & dog become friends & trust each other, there's no getting away from the fact that dogs can see young children as unpredictable. Their movements are more erratic, the signals that your dog picks up from you in the form of body language, tone of voice etc are far more confusing in a young child. So the fact that your dog doesn't like cuddles & fuss from your son is easily understandable. Sometimes children can be unintentionally rough, may accidentally pinch or pull the dog. No blame to child or dog ~ this is just how children behave.

I don't think telling your son off in front of the dog would mean what you intended, as far as your dog is concerned. All your dog would register is your stress, your possibly angry(?) tone of voice ~ but I don't think the dog would associate you telling your son off with your son throwing something at your dog. All it will do is make you seem more unpredictable to your dog.

IMO the best way to handle things is to allow your son to interact with your dog in ways that they BOTH find enjoyable. So playing with toys or throwing a ball may be the most you can expect at the moment.

You could also try letting your son put your dog's food bowl down and feeding her tasty treats now & again. But as for the cuddling & stroking, if your dog is not comfortable with this, then respect her wishes & judgement. She's trying to say, in the only way she knows how, that she doesn't want your child to be too hands-on at the moment, so she avoids close-up interactions. Maybe your son has accidentally hurt your dog in the past, so she's now avoiding that happening again by keeping at arm's length.

It won't be long before your son is old enough to do more with your dog, maybe some gentle grooming with a soft brush or grooming mitt. He's too young to understand how hard he's brushing or touching at the moment, so just be patient & wait till he's a bit older.

I'm sure that they'll bond over time, especially if you make sure that all their interactions are fun & positive.

The thing with children is that they can, as Wilbar has said, be very intense and sudden with their actions. On top of that, in a very general sense, dogs aren't always keen on cuddles anyway - it's a human (primate!) thing

They do "learn" to tolerate or even like and appreciate them, but a comfy, nice cuddle with you may be very different to one with someone unpredictable who, at times, has accidentally hurt her ...

John Fisher always used to say we, as owners, needed to "think dog" and i think this may be one of those times so I'd suggest always keeping an eye, minimising stress, and also giving her a comfy place she likes that she can get away from him.

You may like to read "The Canine Commandments" by kendal Shepherd; written with children in mind, helps to show how dogs and children can get on safely.

Wys
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