Although he is running as a Democrat and therefore must knock Hillary Clinton out of her position as the front runner in the presidential race, Bernie Sanders is a self-declared Socialist and targets the Democratic establishment in general. He is an Independent senator from Vermont who has made many public criticisms in the past about the Democrat Party, not just Hillary in particular.
Yes, Bernie Sanders is venting his frustration at the entire establishment. He does not want to target Hillary specifically because that would not lead to a solution. He is trying to be progressive and mud slinging is not the way to a brighter future. If more "progressive" politicians followed his example, perhaps things would change.
Hillary Clinton would be wise to start distancing herself from the party establishment. Her campaign should make a clean break and condemn some of their actions. Bernie Sanders has been rather successful at addressing the establishment shortcomings including the execution of their rules and their decision to hold many debates on weekends and other non-appealing times. The attempts to make it difficult to give candidates a platform to present their views make it obvious that the party establishment wants this to go away. While this may all be intended to help Hillary, Hillary would be wise to reject the "help" because it's not actually helping her.
Bernie Sanders is targeting the Democratic establishment instead of Hillary Clinton because of his core beliefs. He runs on what he always run on, his integrity. His strategy is by running on a better government system rather than attack ads. They ads only side-track from the real reason people are voting.