On iPad's iBooks, how to make highlighting show up for PDF files?
iBooks for iPad currently doesn't support highlighting in PDFs. However, there are many 3rd party apps like iAnnotate PDF, GoodReader, or PDFpen that support PDF highlighting and annotating. I use GoodReader and I can personally verify that PDF highlights that were made on Mac's Preview do show up on the GoodReader iPad app.



I also tested the DropBox iPad app and PDF highlights do not show up. 

Hopefully, Apple will add PDF highlighting to a future version of iBooks. If enough people request this feature at the Apple feedback site, maybe they will add it in the near future.