'He/She Can't Help It'
The big reason is the stigma that acting strangely has. Those developmentally disabled people who get 'therapies' are very often trained out of behavior that, like my own odd behavior, is harmless (or at least less harmful than a lot of normal behavior that isn't treated by any 'behavior programs'). Flapping your hands (provided you have enough room) isn't going to hurt anyone. Odd social behavior like launching into monologues can easily be dealt with by just negotiating with the other person (like when my father says he needs to concentrate on driving so I should stop talking) just like a lot of typical behavior is negotiated. But I've met a boy whose teacher was constantly interrupting him when he flapped his hands, and heard of people being alotted only 5 minutes per day to talk about their interests - if they're well-behaved. Can you imagine someone telling you to stop every time you fiddled with your hair (or some similar mannerism) or saying you can only talk about things you're interested in during a set 5 minutes every day?
If you are disabled, you are expected to try as hard as you can to conform. If you're mildly disabled, you probably can conform reasonably well in many settings, and even though your disability doesn't disappear, the other people can pretend it has. If you're severely disabled, you can't conform no matter how hard you try, or you may not even realize you're expected to conform.
Most people know that some people can't conform, even if they try their hardest. They're still supposed to try as hard as they can, but society makes some allowances for them because 'they can't help it'. I think this is a big part of why so many people think it so important to define abnormal behaviour as 'voluntary' or 'involuntary' instead of recognizing that it's really a spectrum, and part of why there's a big division between 'high functioning' and 'low functioning' and between 'bad' and 'disabled' (when the behavior is the same - eg not responding when someone says something to you, or interpreting a command literally when that's not the intended meaning). If you can conform, you should - even when there's no good reason for that particular rule.
Some people who try to train disabled people to conform would protest that 'if they act this way, they'll get teased' (or not be taken seriously, etc). And that is a big part of how society enforces conformity - by rejection and punishment of those who don't conform. But society has two distinct methods of enforcing conformity, and the 'helpers' who try to get us to stop acting weird are using the second method. It is indeed gentler, but that doesn't mean it's OK. The focus is not on those who punish not conforming, but on those who aren't conforming. An analogy that might help illustrate is if you told a gay person 'don't let people know you are gay because some people beat up gays'. That's better than beating them up yourself, but most people these days don't think staying in the closet (conforming) is a good way to solve the problem of homophobic violence.
I've mostly learnt to conform the harder way. I was bullied a lot at school for having unusual interests, running circles around people, getting upset and crying, acting immature, and anything I did that most kids didn't do (or that I did differently, such as being clumsy and awkward in physical activities). My teachers bullied me as well - telling me that I was doing math wrong when I followed different steps or didn't 'show my work', trying to make me stop being interested in the topics I was interested in, etc - but even if they hadn't, the fact that they focused on me instead of the bullies in their attempts to stop the bullying sent the same general message. In public, if I flap my hands or squeal, people stare at me and sometimes act scared of me.
I can control these odd behaviors for the most part, and more importantly to our society, I look like I can control them. I look normal - not just my physical appearance, but also that my speech and general bearing look (even if I weren't trying to conform) close enough to normal that most people don't realize I'm disabled. Even people who know me for awhile - though they know I'm eccentric - often wouldn't realize I was disabled unless I told them. Actually, by and large, the few people who realized I was disabled without being told (or looking for it, like a psychologist) have been bus drivers, because of my difficulty navigating by bus. Note: even if you are visibly disabled, you can look like you're able to conform in certain ways - eg if you are a well-spoken person in a wheelchair, people are likely to assume you can't control motor problems, but most of them will expect you to refrain from covering your ears and screaming when you hear an alarm go off.