"Ignorant" not even being inherently negative here--although I dislike human tendency to attack something they do not understand. Simply not understanding is not bad, though, it's an opportunity to learn. So let's not attack each other here either, let's just discuss and learn
I have often wondered how the need for service dogs collides with the need to keep animals out of certain places for sanitary/allergy reasons. Not really the same situation but last time I was on a plane (couple of weeks ago) I was sat next to a lady who had a cat with her, in a carrier under the seat. The cat was sedated and sleeping and I actually didn't even know she was there until near the end when we had a rough landing and she woke up. But had I been allergic to cats, this could have been a problem. I guess these things are dealt with on a case-by-case basis.
At any rate, the owner didn't have to be rude about this. Perhaps they could have reached some compromise, like letting the dog stay outside and the man sitting at a table near the window where they could see each other. Or the man just going someplace where his business was more appreciated. It's what I would have done.