I have a similar concern with my own son who is very opinionated, does his own thing and isn't into football and won't be persuaded to be. He's also slightly smaller than average height and hates war games and fighting so doesn't fit in. We have a new child moved to his school who has already been picking on him and bullying him. The school have dealt with this pretty well, but I have now told them I want the two of them kept apart after this child injured my son when he threw something at him in the play ground after being told three times to leave my son alone by the dinner lady.
I have tried to get him interested in martial arts as some kind of self defence, but he just won't as he hates anything fighting related and sees it as fightning. He's not into rough and tumble and hates being teased which also makes him an easy target as he takes things very much to heart.
It is difficult but ignoring it won't make it go away. You have to help him prepare as best you can for what's ahead.
Are there any interests your son does have that you can try and encourage. My son likes sports such as swimming and wall climbing which don't really encourage interaction between him and the other children. He also is very driven and hates to come second (or worse below second!) so finds competitive sports quite tough as a result. He has no problem going up to other children and making friends which helps, but he still has trouble compromising when they want to do something he doesn't and he'd rather be on his own.
I encouraged him to join scouts last year, which he sometimes enjoys and sometimes doesn't. But he went away to scout camp last year and when he came back he had made a couple of good friends with children in his class at school, one of who made no bones about saying to me they hadn't really liked him till they went to camp and spent time together and now they are friends. I do help out at scouts and at camp though to be sure he has the support he needs there when he needs it, but i don't stay overnight at scout camp so he gets plenty of his own space too.
Most of our afterschool clubs are sport related so my son wasn't enjoying them. I took it upon myself to start an afterschool art club he did want to do, an art and crafts club. The response has been overwhelming and I've had to limit the numbers, get more help from another parent so we can have more children at the club and the headteacher tells me it is the most popular after school club with about 25% of the children in the classes it's open to attending this term! So my son is certainly not alone in wanting things other than sports things, and a lot of the biys at the club also say they don't like football.
The school also tried to get a chess club up and running, which my son wanted to join, but the outside company they brought in to run it was too expensive and so they had to cancel it. I am hoping the head teacher will try this again next term as several more children have come forward now saying they'd like to do it.
I also used to make a big effort to encourage friendships, but found that very few parents reciprocated. So now I stick more to the ones that do reciprocate and spending time with his cousins. While he's at a small primary school and fairly protected he is doing ok, but when he heads to secondary school I worry that problems will arise and that he will get bullied. I know he will not do well at the local secondary school, and most of his closest friends parents have also said they don't intend to send their children there for the same reasons i have worries, namely bullying and intimidation. the school has a very poor reputation, but living in a rural place it is very hard to get the children in any otehr school because of the distance issue to the next schhol along. So I have the added worry of trying to get him into the school of my choice which has a higher level of pastoral care and at which i feel he will do better academically as well as socially. I may have to move to achieve this, but financially i can't afford to move right now.
For you i suggest you try speaking to his teacher and see if there is anything they can suggest to help him now and find out which children are going to the same secondary school he is that he is closer too. Maybe you can encourage him to find friends interested in things he is outside of school, whatever it might be (drama, sport, art, model airoplanes, scouts etc). If you are on WTC & CTC you can probably get help towards to cost of afterschool clubs and activities.
Your son is not alone, you just have to find those other children who are 'different' like he is. And i'm afraid that is something you have to be proactive in doing. You also have to encourage his self esteem and make sure he gets to spend time with other children who have similar interests to him and at things he is good at. Your son needs your help to do this.
Best of luck.
Gilly