The most important thing that columns preserve is readable line lengths. If you want to maintain good, readable line lengths on the web, you are going to end up with a relatively thin column and a lot of scrolling. Multiple columns allow us to more efficiently use the visible on screen space while maintaining readability. That seems pretty valuable to me.
A single column can give you that.
Multiple columns seem to me to be fundamentally incompatible with (vertical) scrolling. Yes, they make perfect sense when your pages are fixed-size, and the entire page is visible at once, but when you have a single page of potentially unlimited height, where do you break one column and go on to the next?
I find multiple columns in pdfs very annoying to read as you have to scroll down to the bottom of the page, then back up to start the 2nd column, then scroll down to reach the end of the 2nd column.