they didn't seem to have any reason to defy him. It would have even made sense if Connington was unpopular among citizens of this specific town but he was a lord from another land and he was recently made hand. still that doesn't seem to be the case since his reign was supposedly prosperous for the smallfolk and his madness was only for the nobles he thought to be enemies. It would have been also understandable if Aerys's mental health was so commonly known that his subjects secretly loathed him. It would have made perfect sense if Stoney Sept was in Stormlands considering that it seems Robert had been a good Lord, but it is in Riverlands which I think hadn't even openly declared for Robert in that time yet .
so how did Robert won every single one of the smallfolk over? he does seem to have been a charismatic leader in his youth. Now Stoney Sept is big town, not a small village. At the end they had the usurper hidden in a brothel. They moved him from one secret bolt-hole to the next, always one step ahead of the king’s men. He had even sent men crawling through the sewers, yet somehow Robert still eluded him. His knights went house to house, smashed in every door, peered into every cellar. And so he swept down on Stoney Sept, closed off the town, and began a search.