Tooling is some of the issue imo. HTML/CSS actually includes decent functionality for targeting print in addition to desktop+mobile (not perfect, but quite decent), but the print-centric parts have fairly poor support in most tools. Afaik the only tool that really nails the print-centric parts of CSS, and produces good-looking output, is PrinceXML. It's a good piece of software, but having only one working implementation, which also happens to cost $500/seat for desktop usage or $3800/machine for server usage, isn't an ideal situation for an open standard.
The second-best seems to be http://wkhtmltopdf.org/, which is more or less a headless wrapper around WebKit's renderer. But since WebKit puts most of its development effort into interactive/screen usage, the quality doesn't match PrinceXML yet (though it's improving). As a result I think it's still more common for people who need good-looking, open-source PDF output to use a LaTeX workflow, even where an HTML one might otherwise be more natural.
The second-best seems to be http://wkhtmltopdf.org/, which is more or less a headless wrapper around WebKit's renderer. But since WebKit puts most of its development effort into interactive/screen usage, the quality doesn't match PrinceXML yet (though it's improving). As a result I think it's still more common for people who need good-looking, open-source PDF output to use a LaTeX workflow, even where an HTML one might otherwise be more natural.