My oldest son is the same way. He wouldn't hurt a flea. He is 9 now and we are homeschooling this year, but when he was in kindergarten he rode the bus everyday and was being hit, kicked, tripped, etc. by the older kids. I found out he was going to the back to try and find a seat and this would happen. Pecking order, I guess. I went and talked with the teacher and it didn't stop, so I talked with the principal. He took me out and talked with the bus driver and assigned my son to a front row seat and that stopped it. He also had a girl that "liked" him treat him so mean at recess the next year. She would punch him, trip him, hit him, etc. He ended up in the nurses office once because she pushed him on the pavement. I was furious and had had enough. I called the girl's mom and asked her to talk to her daughter. She said her daughter had told her that he was picking on her! I said, "I would believe that if my son was aggressive, but he won't hurt anyone and has never done anything like that to anyone." I knew her daughter was aggressive, especially toward boys and I wanted it to stop. After that, it stopped.
Through the years he has continued to be bullied. He is very smart and kind to everyone. I ended up putting him into karate in kindergarten because of the bullying and it helped his self confidence. They teach not to ever start a fight but to protect yourself when needed. He was in that for several year, he was a blue belt when he quit because the place ran out of business. But that was the best thing we did for him.
His younger sister, 1 1/2 yrs. younger, loves to pick on him too. He won't fight back when she is pounding on him. I hated to tell him to hit her back, but it got so bad that he needed to show her he wasn't going to take it anymore. After he started sticking up for himself, she stopped. He is getting better at defending himself with words and occasionally with actions only when necessary, which is almost never. But it takes time. Try to instill confidence in him with other areas. The karate instructor told me not to tell him to be aggressive and to encourage hurting others. There has to be a balance. I think it is good for boys to be tender. I always praise my son for his kindness. But I tell him he has a right to stand up for himself and to try and talk it out first. He has a tendency to stuff his feelings inside, and I will sit with him and be patient to wait for an answer to my question of what is going on. He will usually tell me and then we can role play and figure out how to deal with the problem. It is important to keep the communication flowing and help him deal with his hurt feelings. I've always talked with my kids about drugs, drinking, bullying, etc. since they were young. I like them to know they can talk to me about anything and I will listen. Role playing is important too. It is a time where they can get up and say how they feel. I ususally start first and show them what I would say, then encourage them to show me how they would react. We work through problems this way and it gives them confidence when they are away from home. Then they will come home and tell me how it went.
I hope this helps.