They're slowly inventing operating systems, complete with hypervisor technology, with all the gargantuan complexity that it implies, to please big business that wants the client OS to essentially become obsolete.
In this case it's not even an exploit really; more like social engineering. (Tricking users into granting the phishing site unrestricted access to their Yubikey, then using that access to trick the user into authenticating a login session for the phishing site.)
A browser is more secure than Qubes?
The flaw is in legacy software, not in what is possible. Had humanity spent the effort that was spent on browsers on operating systems instead, we'd have had the same security improvements without all the negatives.