I think the title should be changed. Your question is not about creative founders, but rather system changes.
I think most users accept, like, and even expect some evolution in your startup's product or service. The thing most users don't like is when you change something drastically, when it already worked well.
Justin.tv comes to mind. When they started, their site was about 4 pages, with the home page hosting the video feed and a few others for information. This worked for those who were interested in watching Justin and crew doing whatever it was they were doing. I remember the day they radically changed the design and layout of the site. The entire background changed, some buttons were missing, others were added. They had prepared viewers already, but the initial reaction was largely negative.
The reason for this change was to shift the direction of JTV. Users would browse through hundreds of feeds instead of only one. They would even publish their own feeds, and the site was redesigned to accommodate this.
This was a major change in direction for those who were watching originally, and many didn't like it. What JTV had before worked for what they wanted to do: Watch Justin. Now it became more difficult, but JTV took a calculated risk in making the change, and I think in the end it payed off because what they have now serves more people in more ways.
The difference is between improvements and overhauls. Improvements are expected and encouraged. Overhauls are only for radical changes in direction or to fix something incredibly broken. If it was broken, your users will thank you in the end, it it's a change in direction, you're taking a risk, and good luck with it.