It's weird for a server to make the assumption that a dinner doesn't want the coin change, and it would likely be something I'd notice. However, I would have very little interest in doing anything about it. When I go out to eat, I assume tip as part of the cost, and I suppose in my mind some of my change does indeed belong to the server. Assuming I was going to tip more than 99 cents, it's just part of doing business, and I would hate to ruin the experience of having a relaxing/fun meal out with complaining to the manager about less than a dollar.
I have found it interesting to hear from the people who would have a stronger reaction that I.