Honestly, one point I don't really see mentioned often regarding Clinton's perceived dishonesty is the power of branding. All decent politicians put a lot of effort and research into building a brand for themselves. The Clintons spent the beginning of their political career and all of the 90s/Bill's presidency building a brand as a new type of Democrat. One openly opposed to the (at the time) perceived excesses and naivete of the more progressive and liberal wing. They were very successful at building the Clinton name as a brand associated with a more moderate, business friendly Democrat.
You can fairly argue that it was necessary, given the contemporary political climate following a series of major defeats; and that this Clinton brand was essential to the democrats' victories in the 90s. But in 2016 things are different, and the base is eager to shed the DLC/moderate/blue dog faction and embrace the progressive/liberal wing again. And Clinton has adjusted her policies accordingly for the most part. But it's not unfair for people to be skeptical of her embrace of the progressive movement when so much effort was put into disassociating the Clinton brand from "liberal" during the 90s when it was more toxic. And the more high profile you are, the harder it is to change those perceptions, or "re-brand."
It's part of why I was wishing for more serious competition against Clinton in the primary. Because it's never made sense to me, from a marketing perspective, to have the embodiment of the 90s/moderate Democrat/Third Way politics lead the charge for the much more progressive direction the party has been taking. But it doesn't help that the current bench of Democrats capable of filling that role is pathetically weak and small due to their complete failure to build up many young stars at the state/local level over the last several years. I think there are definitely steps she can take to improve those perceptions right now, but I would also agree with whoever said that much of it will persist until she can get into office and prove her commitment with more solid actions (which may be very difficult with a Republican congress).
edit: this is also why I definitely agree with royalan that she needs to focus a lot more of her campaign on promoting her current platform. I don't think enough effort has been put in to showing what she has that's new and different from peoples perception of the 90s Clintons. It's why I think she had such a good convention bounce, because the new Democratic platform is popular. It's also why there's such a disparity between Obama's approval and Hillary's polling; because Obama's brand is the embodiment of the new direction of the party. You know, "Change," and all that.