If Uber drivers are private cars, then only a small proportion of them will be able to carry wheelchairs. If they follow the free market, they will charge more. So instead of getting a $20 cab ride to the doctor or a theater, a wheelchair rider may have to pay $50 or $100.
The solution to this is for a company to start up that only caters to disabled passengers, charges the same rates as the other companies, and gets a subsidy from the city. The point is largely moot anyway: many cities already have something like this (though you usually have to call a day in advance), in the form of paratransit services which offer door to door for slightly more than a standard bus fare.