Obviously it is unfair and discriminatory to fire somebody because of their sexual orientation, but put yourself in the business owners situation.
A trans-gender employee in a customer-facing position could very likely be costing the business money. The owner may be the most tolerant, accepting person in the world, but what if the customers aren't? He can't be responsible for their prejudice. He just has to try to run a successful business. Keeping the trans-gender employee in that position may literally drive him out of business. Is that fair?