I agree with you at least in theory. But the issue with web fonts is it's difficult to use them in a way that doesn't harm performance and also doesn't cause flashes of unstyled content. Every time I visit wired.com I find the font transition jarring and unsatisfying, honestly I think they'd be better off with system fonts.

Print media just doesn't have any downsides to custom fonts so there's no reason to not use them.