Comment by bonoboTP

Right, changing the equation fonts may also create ambiguity, some custom, complicated equations (several levels of super and subscript, various bars etc) might use some latex hacks or workarounds.

It would require that the authors also create and polish an HTML version, which is extra work.

Even on the official IEEE sites papers look way worse in the HTML view, even though I guess someone at least tries to tweak the to appear okayish.

Purists would argue to separate the "presentation layer" from the underlying content, but it's never like that in the messy real world. Content and presentation are very much intertwined and abstractions are too leaky.