My pup is like this sometimes too. He doesn't mind getting touched so much, but if you reach down and try to pet him from a standing position he goes into evasive action.
At least when it comes to other people. He'll tolerate a lot more cuddling/petting from me than he will from others.
Either your pup will grow out of it or it's just a permanent fixture of his personality. (I think my own pup will always be semi-aloof with anyone but me.)
I wouldn't worry too much about it. Pups are single-minded and their mother doesn't sit there licking and coddling them constantly, so they don't expect that treatment from their human "moms" either. They'd rather play and explore.