"Rights", for lack of a better term, have a tendency to intersect. And it makes these types of scenarios rather complicated. As an example, "no shirt, no service" - is that an example of discrimination? Technically it is. But I don't think anyone has issue with a restaurant owner or store owner having the right to refuse service to someone based on them being topless! "Rights" do not simply exist for individuals - a business has long had the "right" to refuse service, on most grounds. Notwithstanding any medical exemptions (and I don't even know what that means or entails) that does not necessarily mean a business has to change it's "no mask, no service" policy during Covid. Keep in mind, if the medical exemption means you don't have to wear a mask, that does not automatically mean the medical exemption creates an obligation for every business to allow customers into their stores, if the store has a "no mask, no service" policy! Again, it's alot more complicated than "but I have a doctor's note!" People seem to think that Indigo has to respect the right of "this" potential customer or "that" potential customer - most people forget that Indigo also has to consider the "rights" of their other customers, their employees, etc. The situation is alot more complex than one kid with autism that can't wear a mask.
Having grounds for a claim of discrimination is not the same as a pre-determined 'win' ruling for it. But they are entitled to sue.
Being exempt of mask wearing is not a pass to enter all places without a mask either, no one said that.
1. Discrimination is valid for inherent conditions / characters you cannot easily change about yourself. Being shirtless is not one of them. Being autistic, mute, a certain sex, a certain race, a certain height or age, or asthmatic, are, for contrast. You can't recover from being short, or being being autistic.
2. Discrimination claims are only valid if the concern at hand does not have a strong / plausible reliance on the characteristic being cited as reason for selectivity. For example, you shouldn't be denied to be a phone line customer support agent because you are just too short - that is grounds for a discrimination claim - but you may be lawfully refused if you are a mute, although even that is now being challenged because technology has enabled new possibilities.
3. No one is claiming an exemption means the store, as private business and premises, is required to let exempt persons in. But actions have consequences and we all weigh our options and outcomes for purpose of decision making.
There are expectations of service to the public by businesses. If they offer the same service(s) to all others and the grounds on which you are refused has no bearing on that service or business, and in particular, if they refuse service to you citing a categorical reason, if that reason is a characteristic or property that you cannot easily change about yourself, then the store may be open to claims / damages, while it is their choice to refuse. Again, entitlement to a claim does not mean you always win the claim. Balances of rights come to play.
Freedoms and rights come with responsibilities. Being allowed to do or allowed to refuse to do something, may be your decision, but may also come with consequences or claims from others. It is a balance every person in this system considers in every action they take, daily. This helps the society remain more civil. Just like other rights and freedoms, such as freedom of expression for example. You aren't supposed to be punished just for saying whatever you like to say, but if what you say causes injury to a particular someone, they are equally entitled to sue you for it and claim damages, for example for libel.
Being autistic plays no significant role in browsing a bookstore for books, and the kid wasn't known to actually have covid, but if the store owner specifically just doesn't like the autistic unmasked kid personally, or if the kid or dad was an asshole in how dad treat a staff member for example, or if the kid actually has covid, and one of these is why the store does not let them in, no grounds to claim discrimination.
Yes, the situation is more complicated, but not because it's just one kid versus many scared people, but because nuance in law and balancing of everyone's rights.