Okular (for Kubuntu/KDE) lets you highlight PDFs
I've searched (in vain) several years for an open-source PDF highlighter that runs on Linux.
I'm thrilled to say there is now a (buggy but functional) solution, if you're willing to use KDE/Kubuntu: Okular.
It has some rough edges. Saving files is weird. Saving document XYZ1 as XYZ2 doesn't seem to work, but XYZ1 does seem to save my highlights.
And I don't seem to be able to see my highlights in other PDF readers.
On the plus side, Okular has additional annotation options (that I haven't tried). And it's designed to handle many types of documents (currently in various states of implementation). And the program seems well designed.
Very promising project. And a life-saver for someone like me who wants to highlight 300-page thick Python tutorial PDFs.