If we determine that support IE6 will likely not matter, we break it out as an extra line-item cost and give them the option to support IE6 by paying extra. We explain the facts of their situation and let them make the decision.
It's not about making them feel bad. It's just human nature. It's just a more pleasant experience just paying a price and knowing it'll just work instead of having to pay more than the regular price just to make it work.