I'd suggest having him do something like the 1000 touch drill linked below (or something similar from Coerver). Really mastering at least 3-4 of these moves that he can do at game speed in each direction will do wonders for his confidence. It's free (aren't we paying enough for soccer already?), can be done at home and you can offer incentives to do the drills regularly. After doing the drills several times, practice using them at training and once comfortable in that setting, he'll have the confidence to use those moves in games. NGL, seeing your kids work hard at these and then leave someone's "lingerie on the deck" (Bill Raftery) after using them in a match is awesome.
https://www.youtube.com/watch?v=5g7ZuQD--6o
Also, try and convince him to focus on defending when he steps b/tw the lines every time, without exception. He doesn't even need to be a great defender, but if he is relentless in trying to win 50/50 balls, closes quickly so that opponent needs to get rid of the ball even a half second sooner, etc. he will make an impact on the game. Might create some turnovers and teammates and coaches will notice and appreciate his work rate.
If he's a little timid physically, I wouldn't sweat that too much if he's fairly young. What ultimately happens in most cases (esp as you move up to higher levels) is kids get tired of being pushed around and they are motivated to left weights, get stronger another way or just deliver some blows themselves.
Hope that helps and don't worry about any of this too much - getting better and more confident playing the game is a process and it sounds like he's hungry enough to want to impact the matches, so you've already won half the battle.