PDF is not just designed for printing. It is a format for displaying electronic documents, independently of hardware (printer, screen, e-reader, smartphone, projector etc.) and software (such as the operating system). This format is both good for printouts and presentation, so a good choice as output format.
Presentations with technical or scientific content are often based on documents, very often written in LaTeX also because of it's mathematical typesetting capabilities. It's very natural to use the same tool, LaTeX, for the presentation.
The benefits of LaTeX, such as separating the form/style and the content, portability in source, implementation and output, cross-referencing capabilities and typesetting quality, are great for presentations as well.
As I use LaTeX, I can work on the source using Windows, Linux, or Mac OS X, and I can give the presentation away as a PDF for reading or presenting on a conference, the reader or speaker can use Windows, Linux, Mac OS X, a tablet computer, a smartphone - or a printout.
If I would use PowerPoint - well, I would be pretty bound to Windows Version X with PowerPoint Version Y or a suited viewer, which is also a limit for the reader or presenter.
Best Answer
My favorite (so far, I haven't tried them all) is beamer.
Beamer page on CTAN
Beamer homepage on github
There are lots of beautiful templates you can choose from and it's very customizable. It also seems to be widely used so you can find help online.