I also adopted 2 schnoodles last month and they are still a little scared. I really think they were beaten and neglected where they were. At first they felt comfortable in the house when they thought we were not around. If they saw us they would stop playing and lie down. Now they play with us especially with pretending to bite my hand. But if I go to pet them on top of their head they run away. They are ok with petting them everywhere else but the top of their heads.
My advice is to just give it some time. Play with him with a toy rope, and try to gain his trust. Don't give up. He's much better off with you than on the shelter. Just have patience...:)