Genealogy software files store the data in a database -- PAF stores data as a GEDCOM, a generic genealogy data file that can be exported to other genealogy software.
FTM (Family TreeMaker) -- stores data as an FTM file, but the dataset can be exported in various forms.The export from FTM as a GEDCOM(PAF type) is not a true PAF-Gedcom and some info such as notes, sources, etc. may not convert.
I think most folks prefer whichever software they've used most, although some later evolve to more advanced and complex genealogy programs.
I started with PAF years ago before they had a user guide or tutorial, and have used FTM briefly -- but I greatly prefer PAF.Folks who started with FTM prefer that.