To use Xournal to highlight or add text to a PDF file, select File >
Annotate PDF (you can also chose the usual File > Open, but make sure
you then select to view all files, not just Xournal files) and select
the PDF you want to annotate or highlight text.
Xournal cannot save a file in PDF format but you can easily select
File > Export to PDF to achieve something similar so it's a viable
solution for those who are looking for a reliable tool to
annotate/highlight text in PDF files on Linux.