Yes. She would have been viewed differently. Some people say that people would not have disliked her for being so ruthless and having no remorse of her actions. That may be true to an extent. But I also feel people would have seen the selfish reasons behind all the humanitarian things she was doing in Essos. She helped the masses to come to power and burned anyone who opposed her. The masters who were crucified at Mereen, the witch who killed Drogo, the people killed in Astapor were shown to be 'bad'...but then is it even fair to overlook the fact that they were all those who opposed her? It was only at the time of Tarlys' execution that it becomes apparent that Daenerys doesn't only kill those who are treating the slaves and poor badly, but basically anyone who refuses to bow down to her. So yes, had Daenerys been a man, people would have seen her differently. She wouldn't be treated like a goddess, but a dictator who gained power because he had the masses supporting him.