Not to be dismissive of a chunk of philosophy, but your post is akin to "I've tried to understand elan vital, but I keep running into problems integrating it with my biology course".
Materialists should be able to answer "why do people think they have qualia" without it being a mystery.
I encounter many intelligent people (not usually LWers, though) who say that despite our recent scientific advances, human consciousness remains a mystery and currently intractable to science. This is wrong. Empirically distinguishable theories of consciousness have been around for at least 15 years, and the data are beginning to favor some theories over others. For a recent example, see this August 2011 article from Lau & Rosenthal in Trends in Cognitive Sciences, one of my favorite journals. (Review articles, yay!)
Abstract: