That's how academic papers are done. One reason is that it's more complicated to do mathematical equations and such in HTML (we don't even talk about text) than it is to simply use LaTeX.
I understand the need for proper formatting in academic papers, but it wouldn't hurt anyone to provide a text copy after the fact.
If someone needs a formula they can render the pdf. But a secondary text copy can be more easily indexed, searched and viewed on any kind of text-viewing device... it's just a million times more convenient.
It "hurts" in that it takes time. It's also not just math, but figures as well - diagrams and experimental results. There are automatic Latex-to-HTML programs, but their results are not pleasant. And I have difficulty putting up things that are ugly.
In recent Firefoxes, they get transparently converted to HTML by PDF.js, so I don't tend to care too much either way. There's a little bit of conversion overhead, but then there would also be some conversion overhead if they were using MathJax.
A similarly off-topic question: Why isn't "automatically crop margins" a standard feature on all PDF viewers?
I don't care if it perfectly matches the way the PDF is supposed to look printed out, I just want to read the paper. I can scroll through web pages and flip through PDF pages just fine, but I loathe mixing the two metaphors, so I have to be in "fit page" mode. I'd find entire pages of PDFs perfectly legible on my 11' netbook or 6' e-reader, if only the damned things would crop out all of that wasted blank space and use their entire screens for the content.
No, the zoom feature on most PDF readers is not adequate, because you then lose the ability to progress exactly one page forward and backward at a time (at least, this is the case on every reader I've used). Not to mention, who wants to do that manually every time they want to read a paper?
And I enjoy PDFs on my Retina iPad. Much better than other text representations, almost sharp as on the paper, the screen format matches the paper format, it's easy to move the whole PDF to iBooks for later reading. Perfect.
Mainly because most math/CS papers have a lot of LaTeX in them for equations and symbols, so it makes sense to write the entire paper in LaTeX and then convert to PDF or PS.
