Realistically, it's probably less that Clinton had the entire system rigged in her favor, and more just that the Democrats were afraid of nominating Bernie because they didn't want to commit to backing up his policy proposals if he was elected. Sanders' ideas might be popular but most of them wouldn't be able to get past Republican obstruction, and the Democrats were probably wary of blowing what little political capital they had on policies that had little chance of getting through. Also, they were probably afraid of the potential for infighting within the party between moderates and progressives, since they can already see how intra-party factionalism has driven the Republicans off a cliff in the last few years.