In the hope that someone has an insight, I have experimented a little to provide more information. First, here is the code of a short XHTML file produced (in part) with Save As in Mathematica:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1 plus MathML 2.0//EN"
<!-- Created with the Wolfram Language : www.wolfram.com -->
var cdf = new cdfplugin();
cdf.embed('HTMLFiles/Calculus Summary_1.cdf', 600, 400);
<p>Well, at least this works:</p>
<embed src="HTMLFiles/Calculus Summary_1.cdf" width="600" height="400"></embed>