What you need to keep in mind with bearded dragons is that the flight instinct is what keeps them alive in the wild, especially when they're so young, small and defenseless. He won't let you pick him up because he still thinks you could be a predator.
It's hard, but the only real answer to getting him to adjust to being handled is time and perseverance. You have to be patient. Bearded dragons, really reptiles in general, aren't like dogs and cats where there's a quick and easy bond between them and humans — you need to teach them slowly over time that you aren't a threat.
To give you some perspective: I've had my beardie for two months, and he was owned by a family member before me for one month. He used to puff up, hiss, and run from me. He doesn't do that anymore, but even though he's been with me for two months, he'll still sometimes get nervous when I reach for him. I can tell by his body language — he gets still, looks down, and just kind of freezes. He also still sometimes closes one eye at me, which is typically an indication that he wants me to go away. This is after two months of handling him every single day and following all the tips and tricks to get him adjusted.
But every day is an improvement. Like I said, he doesn't hiss or puff up anymore. When I have him out of his viv, he'll explore a room and then come back and climb on me. Sometimes he'll just perch on my shoulder or head (if you ever let yours do this make sure you have something soft underneath you in case he jumps), or he'll snuggle into my neck. He lets me touch him all over without running away, and will sometimes just sit on my knee and tilt his head at me while I talk to him.
It isn't an instant process, and you just need to keep that in mind and not get discouraged.
Make sure, though, that when you do reach for him you're not swooping down from above (come at him from the side as best you can).