I've read about this before. In Minneapolis there are some drivers with doctors' notes and you are supposed to tell the dispatcher that you have a dog so that they can be sure to not send one of those drivers. In Cincinnati there was a lawsuit filed over this and the city decided that unless the driver could prove that their allergy was so severe that it rose to the level of itself being an ADA disability, they could not use it as a reason to refuse fare.

http://www.nagdu.org/taxis.html

http://www.jsonline.com/news/milwaukee/29312754.html

In one case it is explicitly mentioned, and in another tangentially, that some people have refused rides to people with dogs on religious grounds as Islam considers contact with dogs to be very objectionable, using allergies as an excuse. I read the recent filing and it didn't mention anything specifically about that though. Included below for completeness:

http://pdfserver.amlaw.com/ca/NationalFederationoftheBlindvU...

Read "Where Service Animals Are Allowed" at [1]. My understanding is that a driver with allergens would not be required to take the dog the same way they can exclude a dog from a burn unit. However making a false claim about such things would be against the law.

http://www.ada.gov/service_animals_2010.htm

That might be the reason that service dogs are typically of breeds that are least likely to cause allergic reactions.