I fully understand the OP's concerns.
Our son was exactly the same, he preferred girls and has never had any real friends who are boys. It was fine in the early years at primary school, but in the later years and then in secondary school, he was definitely lonely, as the girls just did their own thing and stayed in "girl's" cliques except when it came to chasing after boys!! It was ironic really because he liked "male" things like football but didn't like the boys who were into football as he thought them too rough/rowdy etc so he'd watch footie on TV on his own or play on his own in the garden! Girls always liked him as a friend, but he never got invited for parties/ activities, etc.
He came into his own at Uni sharing a flat with other girls. In his first year, it was 4 boys/4 girls, but as expected, he didn't really have anything in common with the boys so he didn't do anything with them, didn't go out with them. He didn't argue or fall out with them. He got on very well with the girls, I think they liked him because he's friendly, honest, helpful, etc. By the third year, the girls had joined some others and were renting together, and invited him to join them as the only boy in a flat with 7 other girls!! Nothing romantic (don't think so anyway), but they absolutely loved him living with them. But still the same scenario, they'd go out and do their own thing, go to parties, socialising, etc., but they'd never invite him along which he was sad about, but at least he enjoyed living with them as they did movie nights, cooked group meals together, etc.
It's such a shame, but the trouble is that a lot of boys are pretty rough, loud, boistrous, and some lads just don't like that. Unfortunately, they start to be labelled as gay or soft etc., which is very unfair. Like here on MN, so many people criticise blokes for their actions etc., so we should all be encouraging "gentle" boys to be themselves and support them as they're the ones who'll turn into a better "standard" of future husband/partner/father material than the stereotypical "lads will be lads" that we applaud in childhood and then bitterly complain about as adults!