After being bitten by this on two sites in the past few days, I'd suggest adding the following to the uninstall instructions (other notes):
- Flush your permalink cache.
When you remove the .htaccess rules generated by WP Super Cache, all permalinks may stop working. Except for the home page (which makes it really easy to miss at first sight). Changing the permalink settings to something else and back to your previous setting (hit save each time) solves the problem instantly.
Hope this helps, and thanks for this awesome plugin!