As I understand it: guide animals are generally trained to know when they're "at work" and when it isn't. When "at work", the guide animal is not given affection because it needs to be focused on its task. This is why seeing eye dogs have "don't pet me" signs on them: any kind of affection is a distraction from the necessary task of helping the owner.

When not "at work" (usually there is some signal), it obviously depends on the owner; but most of the disabled people I know pamper and love these animals to death, and they are extremely well treated. They are simply only showered with affection in private, when not expected to be focused.