According to causal theories of content, what makes my beliefs be about, say, horses is that the beliefs have the right causal connection with horses. Of course, there are going to be harder cases: I also have beliefs about unicorns, namely that they do no exist, and these beliefs do not have a causal connection with unicorns. But the unicorn beliefs get their intentionality derivatively from other thoughts, like those of animals and horns, from which they are constituted, derived, etc.
Now, beliefs about qualia are not constituted, derived, etc. from thoughts about non-qualia. So by causal theories of content, my beliefs about qualia have to have the right causal connections with qualia. So, causal theories of content are incompatible with epiphenomenalism, since according to epiphenomenalism qualia aren't causes.
Causal theories of content are the materialist's best bet for a theory of content. Qualia are meant to be a very modest addition to the materialist's story. But they aren't a modest addition—they require a revision of the theory of content.