If you find that your WP Super Cache plugin isn’t working, be sure you have something in the Accepted Filenames & Rejected URIs text box. A few months ago, when I first started playing around with this plugin, it took me quite a while to figure out that something needed to be in the field for the plugin to work.
By default, both wp-. and index.html are included, but I removed them (for various reasons that aren’t worth getting into here) on the assumption that leaving the text box blank would cause everything routed through WP to be cached. Apparently though, the plugin treats empty space there as a directive to not cache anything, and so my blank text box was causing the plugin to have zero effect on my site (though the same can’t be said for my sanity).
Put something in the field (e.g., gobbledygook) and you should be good to go.