Some pups/dogs just don't care for physical attention. Forcing them to cuddle, or be pet etc. will only enforce their need to be away from you.
My GSD will lay next to me contently. The moment I start scratching his head, he'll get up and walk away. He'll remain in the same room and follow me if I should leave the room, but he's not really into being physical. (But, he'll stand for hours if I scratch his butt.)
My Lacy (18 months) reads any physical contact as the invite for play. That is HIS favorite thing, why should he think I would think any differently? So I make it a point to give a pat or rub his ear and leave it at that.
What I do is I talk to them all the time. To my Lacy, I'm a walking Pez dispenser. The moment the does a desired task he gets a treat. If I'm doing laundry and drop a sock, he'll pick it up and follow me. He gets a treat. If I go into another room and he follows me, I'll reward. If he picks up my shoe and I tell him to 'leave it' and he drops it, he gets a reward. Ect. Because I always interact with him, he finds me interesting. He follows me waiting for me to ask him for something to do. In passing, I'll give a rub or a pat. But I don't hold him or force him to be still so I can provide physical contact.
For Hondo (GSD) he simply loves to me spoken to. So I'll carry on a conversation with him. "Hey boy, I need to go outside for a minute. You wanna go?" "Hey bud, did you see where the remote went?" Silly things. But that is what HE likes. Sometimes he'll come to me for a ear rub. But again, I never force physical attention on him.
Don't assume because you like to be physical, that your dog/pup would like it as well.