I know this is a bit of a n00b question but if they PPD sites pay you every time someone downloads one of your files, how do they make any money? I assume they have some kind of advertising on the download pages?

Most of the PPD sites like Cleanfiles,etc are just affiliates.

They get offers from CPA companies and they create their own locker for downloading files.

After someone completes an offer they pay you after taking their cut.